Mol Hortic. 2025 Oct 10;5(1):55. doi: 10.1186/s43897-025-00177-9.

ABSTRACT

Citrate is critical to the flavor of horticultural fruit and governed by ACO. However, the specific ACO and its upstream regulators involved in citrate metabolism during pear (Pyrus spp.) fruit development remained uncharacterized. This study identified and characterized six PbrACOs from the Pyrus bretschneideri Rehd. genome. Comprehensive analyses of citrate levels, cyt/mitACO activities, and PbrACOs expression profiles in the pericarp and cortex tissues of developing ‘Yali’ and ‘Dangshansuli’ fruits revealed PbrACO2 as a candidate gene. Subsequently, PbrACO2 was confirmed as a mitochondrial aconitase catalyzing citrate-to-isocitrate conversion in vitro and in vivo. Analysis of differentially expressed transcription factors (TFs) and cis-acting elements in the PbrACO2 promoter identified nuclear PbrMYB3 and PbrMYB65, derived from whole genome duplication/segmental duplication, as candidate upstream regulators. These MYB TFs, without direct relationship, bound, as monomers, to the same two MYB-binding sites in the PbrACO2 promoter to activate its transcription, thereby promoting citrate isomerization in pear and tomato. Further investigation revealed that PbrMYB3 and PbrMYB65 are transcriptionally regulated by PbrNAC34a. Given their tissue-dependent expression profiles, the PbrNAC34a-PbrMYB3/65-PbrACO2 cascade partially accounts for citrate differences between pear fruit pericarp and cortex tissues. These findings enhance understanding of citrate accumulation in Rosaceae fruit and provide genetic resources for pear breeding.

PMID:41068843 | DOI:10.1186/s43897-025-00177-9

Physiol Plant. 2025 Sep-Oct;177(5):e70568. doi: 10.1111/ppl.70568.

ABSTRACT

One of the major disfunctions in heat-stressed plants is enhanced protein damage. Creeping bentgrass (Agrositis stolonifera L.) is an economically important perennial grass species but it is sensitive to high temperatures. Several experimental lines of creeping bentgrass varied in response for physiological traits, total protein content, and protein degradation rates in response to heat stress. The ubiquitin-proteasome system plays a crucial role in the removal of damaged proteins, and there is a critical need to better understand the changes in proteins that occur during heat stress. Hence, we aimed to estimate change in global protein accumulations by performing gel-free proteomics, and polyubiquitin-omics to identify proteins that have been polyubiquitinated and targeted to the ubiquitin-proteasome system with Tandem Ubiquitin Binding Entities in contrasting lines exposed to heat. We found that metabolic processes, like photosynthesis, antioxidant defense and protein refolding could be regulating heat tolerance in creeping bentgrass. Heat-tolerant line S11 729-10 was able to maintain proteins involved in the light reactions of photosynthesis, while enhancing antioxidant proteins, particularly during the later phase of heat stress. This contributed to its improved performance, including greater cell membrane integrity as well as healthier light harvesting components. Additionally, the faster turnover of key polyubiquitinated antioxidant proteins in S11 729-10 likely represents a critical mechanism for protecting against oxidative damage. This is the first time that polyubiquitin-omics has been utilized in turfgrass. These findings provide insights into protein metabolism during heat stress that could be utilized to help develop new cultivars with enhanced tolerance to heat.

PMID:41070926 | DOI:10.1111/ppl.70568

Commun Psychol. 2025 Oct 7;3(1):145. doi: 10.1038/s44271-025-00324-4.

ABSTRACT

Every social situation that people encounter in their daily lives comes with a set of unwritten rules about what behavior is considered appropriate or inappropriate. These everyday norms can vary across societies: some societies may have more permissive norms in general or for certain behaviors, or for certain behaviors in specific situations. In a preregistered survey of 25,422 participants across 90 societies, we map societal differences in 150 everyday norms and show that they can be explained by how societies prioritize individualizing moral foundations such as care and liberty versus binding moral foundations such as purity. Specifically, societies with more individualistic morality tend to have more permissive norms in general (greater liberty) and especially for behaviors deemed vulgar (less purity), but they exhibit less permissive norms for behaviors perceived to have negative consequences in specific situations (greater care). By comparing our data with available data collected twenty years ago, we find a global pattern of change toward more permissive norms overall but less permissive norms for the most vulgar and inconsiderate behaviors. This study explains how social norms vary across behaviors, situations, societies, and time.

PMID:41057696 | DOI:10.1038/s44271-025-00324-4

Nat Plants. 2025 Oct 3. doi: 10.1038/s41477-025-02122-6. Online ahead of print.

ABSTRACT

Iridoids are specialized monoterpenes ancestral to asterid flowering plants^1,2 that play key roles in defence and are also essential precursors for pharmacologically important alkaloids^3,4. The biosynthesis of all iridoids involves the cyclization of the reactive biosynthetic intermediate 8-oxocitronellyl enol. Here, using a variety of approaches including single-nuclei sequencing, we report the discovery of iridoid cyclases from a phylogenetically broad sample of asterid species that synthesize iridoids. We show that these enzymes catalyse formation of 7S-cis-trans and 7R-cis-cis nepetalactol, the two major iridoid stereoisomers found in plants. Our work uncovers a key missing step in the otherwise well-characterized early iridoid biosynthesis pathway in asterids. This discovery unlocks the possibility to generate previously inaccessible iridoid stereoisomers, which will enable metabolic engineering for the sustainable production of valuable iridoid and iridoid-derived compounds.

PMID:41044409 | DOI:10.1038/s41477-025-02122-6

Front Plant Sci. 2025 Sep 16;16:1657140. doi: 10.3389/fpls.2025.1657140. eCollection 2025.

ABSTRACT

In reciprocal interspecific near-isogenic lines developed by crossing elite cultivars Acala Maxxa (Gossypium hirsutum) and Pima S6 (G. barbadense) representing the two major domesticated species of cotton, we identified genomic locations underpinning an important fiber quality trait – fiber elongation (ELO). Phenotypic evaluation of these lines in three environments revealed a total of 36 QTLs, including 14 (38.89%) on the D subgenome, from a progenitor that does not produce spinnable fiber. Nearly half (16, 44.4%) of the 36 QTLs identified in the study explained less than 6% of phenotypic variation, and two (EL07.1 and EL25.1) were new, justifying the use of near-isogenic lines for analysis. Significantly larger additive effects of these QTLs in comparison to those reported using early generation backcrosses, F₂ and F₂ derived populations as well as recombinant inbred lines (RILs) show that NILs offer an advantage in estimating more precise QTL effects by removing background noise due to segregating genomic regions. Seven genomic regions on chromosomes 2, 6, 9, 12, 15 and 18 were consistently associated with ELO in two of the three environments tested. A total of 11 (30.56% of) QTLs had transgressive allele effects, i.e. which were opposite of what would be predicted from the parental phenotypes, indicating opportunities to breed superior interspecific lines; and three QTLs (8.33%) had heterotic alleles that may contribute to the striking fiber quality of F₁ hybrids between these species. Limited reciprocity of QTLs in the two backgrounds is attributed to the combined consequences of epistasis, small phenotypic effects and imperfect coverage of donor chromatin in the recipient background. The availability of DNA markers linked to both G. barbadense and G. hirsutum QTLs identified in this and other studies promise to assist breeders in transferring and maintaining valuable traits from exotic sources during cultivar development.

PMID:41036399 | PMC:PMC12479486 | DOI:10.3389/fpls.2025.1657140

mBio. 2025 Sep 30:e0150525. doi: 10.1128/mbio.01505-25. Online ahead of print.

ABSTRACT

In most branches of the fungal kingdom, sexual development marks a dramatic shift from simple multicellular hyphae to complex fruiting bodies composed of multiple tissues and cell types. It is essential to tightly regulate development to prevent unnecessary energy investment into building these structures. Polycomb repressive complex 2 (PRC2) is a highly conserved regulator of development in multicellular organisms. In plants, animals, and some fungi, PRC2 tri-methylates histone H3 lysine 27 in promoters and gene bodies to repress gene expression. In Neurospora crassa, H3K27me3-associated genes are poorly conserved and stably repressed in standard lab conditions. Through analysis of publicly available RNA-seq experiments, we found that PRC2-methylated genes are specifically activated during sexual development. PRC2-methylated genes comprise a distinct subset of developmentally induced genes (DIGs) characterized by an exceptionally high degree of cell-type specificity. Loss of PRC2 activity results in the precocious formation of perithecia-like structures (dubbed false perithecia), even in the absence of a compatible mating-type partner. These structures show a unique gene expression profile with the activation of both PRC2-methylated and unmethylated DIGs, suggesting that loss of PRC2 leads to a major transcriptional reprogramming event. Together, these data suggest that PRC2 is part of a developmental checkpoint that restricts fruiting body development to the appropriate conditions.IMPORTANCEDevelopment of multicellular eukaryotes involves transcriptional reprogramming to drive cell fate transitions. This study identified PRC2 as a critical regulator of cell fate in the model filamentous fungus Neurospora crassa, where it silences a subset of sexual development genes. Loss of regulation by PRC2 triggers a major reprogramming event in which genes specifying sexual tissues cannot be repressed, causing a homeotic transition. These results provide novel insights into the role of PRC2-mediated regulation in the fungal kingdom and uncover a critical checkpoint regulating complex multicellular development.

PMID:41025791 | DOI:10.1128/mbio.01505-25

Proc Natl Acad Sci U S A. 2025 Oct 7;122(40):e2503876122. doi: 10.1073/pnas.2503876122. Epub 2025 Sep 29.

ABSTRACT

Polycomb group (PcG) proteins form chromatin modifying complexes that stably repress lineage- or context-specific genes in animals, plants, and some fungi. Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) to assemble repressive chromatin. In the model fungus Neurospora crassa, H3K27me3 deposition is regulated by the H3K36 methyltransferase ASH1 and components of constitutive heterochromatin including the H3K9me3-binding protein HETEROCHROMATIN PROTEIN 1 (HP1). Hypoacetylated histones are a defining feature of both constitutive heterochromatin and PcG-repressed chromatin, but how histone deacetylases (HDACs) contribute to normal H3K27me3 and transcriptional repression within PcG-repressed chromatin is poorly understood. We performed a genetic screen to identify HDACs required for repression of PRC2-methylated genes. In the absence of HISTONE DEACETYLASE-1 (HDA-1), PRC2-methylated genes were activated and H3K27me3 was depleted from typical PRC2-targeted regions. At constitutive heterochromatin, HDA-1 deficient cells displayed reduced H3K9me3, hyperacetylation, and aberrant enrichment of H3K27me3 and H3K36me3. CHROMODOMAIN PROTEIN-2 (CDP-2) is required to target HDA-1 to constitutive heterochromatin and is also required for normal H3K27me3 patterns. Patterns of aberrant H3K27me3 were distinct in isogenic ∆hda-1 strains, suggesting that loss of HDA-1 causes stochastic or progressive epigenome dysfunction. To test this, we constructed a new Δhda-1 strain and performed a laboratory “aging” experiment. Deletion of hda-1 led to progressive epigenome decay over hundreds of nuclear divisions. Together, our data indicate that HDA-1 is a critical regulator of epigenome stability in N. crassa.

PMID:41021810 | DOI:10.1073/pnas.2503876122

Theor Appl Genet. 2025 Sep 27;138(10):260. doi: 10.1007/s00122-025-05043-2.

ABSTRACT

Exotic Gossypium accessions still harbor QTL‑validated alleles that, combined with CRISPR pyramiding and genomic selection, can break the entrenched fiber length-strength trade‑off. Cotton’s four independent domestications twice in diploids and twice in allotetraploids offer a natural experiment in fiber improvement. Synthesizing three decades of data, we chart how polyploidy, selection and modern breeding have repeatedly reshaped the Gossypium genome. More than 15,000 quantitative trait locus (QTL) and genome wide association mapping studies (GWAS) hits converge on a handful of chromosomal “hotspots”; new MAGIC, NAM, NIL and long-read resources now narrow these peaks to < 200 kb, resolving causal genes such as GhHOX3, GhZF14 and GhMYB7. Multi-omics evidence links auxin, ethylene, gibberellin, brassinosteroid and strigolactone signaling to HDZIP IV, MYB, bHLH/HLH and ERF networks that drive fiber initiation, extreme cell elongation and cellulose deposition. Population genomics shows that ~ 40% of favorable fiber alleles are fixed in elite Gossypium hirsutum, yet wild diploids and landraces still harbor variants that could break the length strength trade-off. We propose a three-step roadmap genomic selection, CRISPR gene pyramiding and accelerated introgression to expand cotton’s genetic base and deliver fibers suited to sustainable textile demands.

PMID:41014362 | DOI:10.1007/s00122-025-05043-2

Fungal Genet Biol. 2025 Sep 23:104038. doi: 10.1016/j.fgb.2025.104038. Online ahead of print.

ABSTRACT

Nitrous oxide (N₂O) derived from agricultural activity is a major contributor to Earth’s greenhouse effect. Synthetic nitrogen fertilizer applied at high levels, particularly combined with heavy rainfall events, generates hot spots of N₂O emissions in agricultural fields due to the process of microbial denitrification. Here, a key conserved fungal denitrification enzyme necessary for N₂O emissions was identified. Phylogenetic analysis revealed that fungal NOR1-like genes, with rare exceptions, are highly conserved and confined to the phylum Ascomycota. Plant pathogenic Fusarium species that possess NOR1 exhibited drastic differences in N₂O production based on denitrification potential. Functional characterization of the p450nor nitric oxide reductase encoding gene, NOR1, in the soil-borne denitrifying maize pathogen, Fusarium verticillioides, showed that this enzyme is critical for fungal N₂O production. Deletion of the single copy NOR1 gene in F. verticillioides eliminated N₂O emissions. Complementation of deletion mutants via the NOR1 gene add-back restored wild type N₂O emission levels and segregation analysis further corroborated the pivotal role of NOR1 for N₂O emissions. We suggest targeting of the NOR1 enzyme as an effective strategy to reduce fungal-based N₂O emissions.

PMID:40998212 | DOI:10.1016/j.fgb.2025.104038

Plant Cell Physiol. 2025 Sep 26:pcaf122. doi: 10.1093/pcp/pcaf122. Online ahead of print.

ABSTRACT

Plant cell wall polysaccharide glycosyltransferases catalyze the transfer of sugars from specific nucleotide sugar donors onto specific acceptor substrates. The mechanisms of how their enzymatic specificity is determined is one of the long-standing questions in plant cell wall biology. In this report, we studied the biochemical functions of Arabidopsis and poplar GT61 glycosyltransferases involved in xylan substitutions and investigated the molecular determinants of their nucleotide sugar donor specificity. Enzymatic activity assays of recombinant proteins of Arabidopsis and poplar GT61 members demonstrated that two of them, AtX2AT1 and PtrX2AT1, exhibited xylan 2-O-arabinosyltransferase activities specifically using UDP-Araf, two other ones, AtXYXT2/3, possessed xylan 2-O-xylosyltransferase activities specifically using UDP-Xyl, and three other ones, PtrXXAT1/2/3, were able to catalyze the transfer of 2-O-Araf and 2-O-Xyl onto xylan using both UDP-Araf and UDP-Xyl. Structural modeling and molecular docking of PtrXXAT1 identified amino acid residues involved in interacting with UDP-Araf and UDP-Xyl at the putative active site and site-directed mutagenesis revealed their critical roles in PtrXXAT1 catalytic activities. Furthermore, structural alignment and reciprocal swapping of UDP-Xyl-interacting residues of PtrXXAT1 with their corresponding residues of AtX2AT1 pinpointed key residues determining their nucleotide sugar donor specificity. Our results indicate that Arabidopsis and poplar GT61 members catalyze 2-O-Araf- and/or 2-O-Xyl substitutions of xylan and that subtle structural differences in their substrate-binding pockets could alter their substrate specificity toward nucleotide sugar donors.

PMID:41001967 | DOI:10.1093/pcp/pcaf122

Plant J. 2025 Sep;123(6):e70498. doi: 10.1111/tpj.70498.

ABSTRACT

The apoplast is a critical interface in plant-pathogen interactions, particularly in the context of pattern-triggered immunity (PTI), which is initiated by recognition of microbe-associated molecular patterns. Our study characterizes the proteomic profile of the Arabidopsis apoplast during PTI induced by flg22, a 22-amino-acid bacterial flagellin epitope, to elucidate the output of PTI. Apoplastic washing fluid was extracted with minimal cytoplasmic contamination for liquid chromatography-tandem mass spectrometry analysis. By comparing our data to publicly available transcriptome profiles of flg22 treatment from 1 to 18 h, we observed that several highly abundant proteins exhibit relatively unchanged gene expression across all time points. We also observed topological bias in peptide recovery of 19 enriched receptor-like kinases with peptides predominantly recovered from their ectodomains. Notably, tetraspanin 8, an exosome marker, was enriched in PTI samples. We additionally confirmed increased concentrations of exosomes during PTI. This study enhances our understanding of the proteomic changes in the apoplast during plant immune responses and lays the groundwork for future investigations into the molecular mechanisms of plant defense under recognition of pathogen molecular patterns.

PMID:40991770 | DOI:10.1111/tpj.70498

Phytopathology. 2025 Sep 23. doi: 10.1094/PHYTO-05-25-0178-R. Online ahead of print.

ABSTRACT

Pantoea stewartii subspecies indologenes (Psi) isolates can cause disease in several Poaceae hosts, including millets and rice and were recently known to cause foliar and bulb symptoms characteristic of center rot in onions. Cover crops such as millet and cash crops like corn are commonly grown in the summer after onion harvest in Vidalia, Georgia, USA. However, the risk of pathogen transmission to onions in the cropping systems where summer crops precede onion planting is largely understudied. We evaluated the survivability of Psi in corn and pearl millet residues and assessed its ability to colonize onions transplanted into the infested soil. Our microplot study showed that millet and corn residues support the transient survival of Psi. The presence of the pathogen in the soil also overlapped with the presence of onion transplants. However, despite planting onion seedlings in Psi-infested soil, no bacterial colonization was observed in their rhizosphere and foliar surfaces. We further investigated genetic determinants for bacterial survival in millet residue and bare soil by creating deletion mutants of the genes responsible for exopolysaccharides, flagellar motility, quorum sensing and pathogenicity in a Psi pathovar cepacicola strain PNA 14-12. All mutant strains persisted for at least 24 days in millet residue at high population levels and colonies of all the strains remained detectable in bare soil until 44 days. Overall, our findings suggest that the risk of Psi transmission from millet or corn residue to onions appears is considerably low.

PMID:40986336 | DOI:10.1094/PHYTO-05-25-0178-R

Carbohydr Polym. 2025 Nov 15;368(Pt 2):124161. doi: 10.1016/j.carbpol.2025.124161. Epub 2025 Aug 2.

ABSTRACT

Pectin is generally divided into four distinct structural categories, namely homogalacturonan, xylogalacturonan, rhamnogalacturonan I (RG-I) and rhamnogalacturonan II. While much of the structural diversity of homogalacturonan, xylogalacturonan and rhamnogalacturonan II has been elucidated, the structural features of RG-I are less well understood. In this work, we employed multiple complementary analytical techniques to present a detailed structural analysis of RG-I in the model species Arabidopsis thaliana. Starting with highly purified RG-I from different Arabidopsis tissues, we employed comparative linkage and nuclear magnetic resonance analysis along with mass spectrometry analysis of enzymatically digested RG-I oligosaccharides. Besides the presence of the canonical α-1,5-arabinan, β-1,4-galactan, β-1,6-galactan and arabinogalactan RG-I side chains of varying lengths, we show that a large portion of the β-1,6-galactan is terminated by either 4-O-methyl β-glucuronic acid (GlcA) residues or, to a smaller degree, β-GlcA that lacks the Me-ether group. Importantly, O-acetylation of RG-I GalA residues is a minor modification while 10 % of the backbone Rha residues are 3-O-acetylated, and most of the acetylated Rha is additionally branched with β-galactose substituents. Taken together, the combined results of these different analytical techniques present the most comprehensive structural overview of Arabidopsis thaliana RG-I to date.

PMID:40947194 | DOI:10.1016/j.carbpol.2025.124161

Microbiol Resour Announc. 2025 Sep 12:e0008325. doi: 10.1128/mra.00083-25. Online ahead of print.

ABSTRACT

Aspergillus parasiticus is a fungus recognized for producing highly carcinogenic mycotoxins. In this study, we collected 38 isolates of A. parasiticus from fields in South Georgia. We performed whole genome re-sequencing and developed 38 draft genome assemblies of A. parasiticus. The average genome size was 38.7 Mb, with larger genomes (~40 Mb) found in peanut fields in Turner County. Scaffold N50 was recorded highest for isolates collected from the corn fields of Tifton. The average BUSCO completeness score for these assemblies was 99.1%. The genome sequences generated for these 38 isolates will serve as a valuable genomic resource for the community working on aflatoxin mitigation strategies in crops.

PMID:40938094 | DOI:10.1128/mra.00083-25

Front Genet. 2025 Aug 25;16:1626083. doi: 10.3389/fgene.2025.1626083. eCollection 2025.

ABSTRACT

This study introduces a Drought Adaptation Index (DAI), derived from Best Linear Unbiased Prediction (BLUP), as a method to assess drought resilience in switchgrass (Panicum virgatum L.). A panel of 404 genotypes was evaluated under drought-stressed (CV) and well-watered (UC) conditions over four consecutive years (2019-2022). BLUP-estimated biomass yields were used to calculate the DAI, which enabled classification of genotypes into four adaptation groups: very well-adapted, well-adapted, adapted, and unadapted. The DAI was compared with conventional drought tolerance indices, including the Stress Susceptibility Index (SSI), Stress Tolerance Index (STI), Geometric Mean Productivity (GMP), and Yield Stability Index (YSI). Correlation analyses demonstrated strong agreement between DAI and these indices, supporting its validity and consistency. Biplot analyses using the Genotype plus Genotype-by-Environment Interaction (GGE) and Additive Main Effects and Multiplicative Interaction (AMMI) models revealed significant genotype-by-environment interactions (GEI) and identified J222.A, J463.A, and J295.A. A as high-performing genotypes, with J222.A exhibiting greater yield stability across treatments and years. Additionally, DAI isoline curves provided a graphical representation of differential genotype performance under drought and control conditions. These visualizations aided in distinguishing genotypes with stable and superior biomass yield across contrasting environments. Overall, the BLUP-based DAI is a robust and practical selection tool that improves the accuracy of identifying drought-resilient, high-yielding switchgrass genotypes. Its integration into breeding programs offers a comprehensive framework for improving biomass productivity and stress adaptation under variable climatic conditions. The application of DAI supports the development of climate-resilient cultivars and contributes to sustainable bioenergy and forage production systems.

PMID:40927363 | PMC:PMC12414770 | DOI:10.3389/fgene.2025.1626083

Appl Environ Microbiol. 2025 Sep 4:e0108325. doi: 10.1128/aem.01083-25. Online ahead of print.

ABSTRACT

Seeds can serve as a vehicle for the dissemination of pests and pathogens around the world. We recently demonstrated the association of pathogenic Alternaria brassicicola isolates with reduced sensitivity to azoxystrobin (quinone-outside inhibitor [QoI]) in naturally infested commercial broccoli seeds. In this study, we further demonstrate that these isolates were also resistant to two succinate dehydrogenase inhibitor (SDHI) fungicides. Sensitivity of representative A. brassicicola isolates (n = 58) from naturally infested broccoli seedlots to QoI and SDHI fungicides was evaluated under in vitro conditions. Interestingly, 15% (n = 9/58) of the A. brassicicola isolates with reduced sensitivity to azoxystrobin also displayed reduced sensitivity to two commonly used SDHI fungicides (boscalid and penthiopyrad) in broccoli, indicating a potential case of cross-resistance to SDHI fungicides. Ninety-three percent of the isolates (n = 54/58) were resistant to both boscalid and penthiopyrad, while 100% isolates displayed sensitivity to fluopyram. Sequence analysis of sdh genes revealed the presence of only one point mutation (H134R) in the sdhC gene in isolates that displayed resistance to boscalid and penthiopyrad. We also developed and validated allele-specific primers targeting the H134R mutation for rapid screening of SDHI resistance in A. brassicicola. We also found that boscalid-resistant isolates exhibited significantly reduced mycelial growth. However, spore germination rates among different resistant isolates were not different, suggesting that resistant isolates remain competitive in natural populations. Overall, this study provides the first evidence of fungicide resistance to SDHI fungicides in A. brassicicola isolated from naturally infested broccoli seeds and underscores the importance of seeds as a potential source for introducing fungicide resistance across geographical locations.

IMPORTANCE: Alternaria brassicicola is a fungal seed-borne pathogen that can be disseminated via commercial seeds across transplant houses and commercial broccoli fields. Our study provides the first evidence that commercial broccoli seeds can harbor pathogenic A. brassicicola isolates with cross-resistance to two succinate dehydrogenase inhibitor (SDHI) fungicides. We observed that 93% of the A. brassicicola isolates from naturally infested commercial broccoli seeds contained a point mutation that conferred resistance to two SDHI fungicides (boscalid and penthiopyrad). Furthermore, we developed a PCR-based allele-specific assay for the rapid detection and monitoring of fungicide resistance. Our study highlights the importance of seed health testing and potential dissemination of fungicide-resistant isolates locally and globally, thus impacting disease management strategies.

PMID:40905662 | DOI:10.1128/aem.01083-25

Sci Adv. 2025 Sep 5;11(36):eadw7764. doi: 10.1126/sciadv.adw7764. Epub 2025 Sep 3.

ABSTRACT

Respiratory tract infections pose considerable global health challenges. Upper airway colonization is pivotal to these infections, including those caused by Bordetella species. We identified an oligosaccharide, bordetellae colonization oligosaccharide (b-Cool), crucial for early nasal colonization of Bordetella bronchiseptica. We characterized the structure of b-Cool by LC-MS and NMR and found that it is prevalent across a diverse range of bordetellae, including Bordetella pertussis, which causes whooping cough in humans. A B. bronchiseptica mutant lacking b-Cool (Δb-Cool) showed significantly delayed and decreased colonization in mouse nasopharynx and nasal epithelia, resulting in decreased transmission. The colonization defect of Δb-Cool was rescued in mucin deficient mice, suggesting that b-Cool may facilitate colonization in the presence of airway mucins.

PMID:40901963 | DOI:10.1126/sciadv.adw7764

Plant Physiol. 2025 Sep 1:kiaf375. doi: 10.1093/plphys/kiaf375. Online ahead of print.

ABSTRACT

Plant specialized metabolism is intricately regulated and often compartmentalized at the cell-type level. Understanding where and when metabolites accumulate is essential for uncovering their function, biosynthesis, and regulation. Historically, studies have inferred metabolite localization based on the expression patterns of genes encoding biosynthetic enzymes, but these approaches fall short due to the complexity of metabolite transport and the discrepancy between transcript, protein, and metabolite abundance. Recent advances in mass spectrometry imaging, single-cell transcriptomics, and multi-omics have enabled the direct visualization and quantification of metabolites and gene expression at cellular resolution. These technologies have revealed striking cell type- and organ-specific patterns of metabolite accumulation, as well as the underlying transcriptional and chromatin regulatory networks. In this review, we describe case studies in several model and medicinal plant species that highlight the roles of rare or specialized cell types in specialized metabolite biosynthesis and the importance of spatiotemporal regulation. In addition, we discuss why it is becoming increasingly important to transition from single- to multi-omics approaches. As new tools continue to evolve, the regulation of plant metabolism will be uncovered at higher resolution, enabling precise pathway discovery and metabolic engineering for agriculture, biotechnology, and medicine.

PMID:40889291 | DOI:10.1093/plphys/kiaf375

Plant Dis. 2025 Aug 26. doi: 10.1094/PDIS-03-25-0469-RE. Online ahead of print.

ABSTRACT

The severity of tomato yellow leaf curl disease (TYLCD) caused by tomato yellow leaf curl virus (TYLCV) in commercially grown tomato cultivars has been increasingly exacerbated in recent years in the southeastern United States. Four research trials were conducted over two consecutive fall seasons in the years 2022 and 2023 to assess the performance of tomato (Solanum lycopersicum L.) cultivars introgressed with single (Ty-1) or combinations of (Ty-3 and Ty-6) resistance gene(s) in Georgia, USA. In 2022, studies were conducted on a commercial farm in Colquitt County and a research farm in Tift County. In 2023, experiments were performed on a commercial farm in Grady County and a Tift County research farm. Tomato cultivars (cv.) with an intermediate resistance to tomato yellow leaf curl virus (TYLCV-IR), including Camaro, Grand Marshall, Jolene, Red Snapper, STM 2255, and Varsity, were compared to the TYLCV-susceptible (TYLCV-s) cv. Myrtle. This study evaluates the total produced yield of tomato cv. under natural disease incidence, severity, relative maturity and marketable yield. Our findings suggest TYLCV-IR cv. STM 2255, Jolene and Grand Marshall, except Red Snapper, had a lower virus incidence compared to cv. Myrtle. Moreover, cv. Red Snapper, Varsity and Camaro exhibited moderate disease progression in our research plots. The cultivars Grand Marshall and Jolene had significantly lower TYLCD severity than Myrtle. Furthermore, fruit yields per plant were highest for Camaro, Grand Marshall, Jolene, and STM 2255. Overall, Camaro, Grand Marshall, Jolene, and STM 2255 performed the best based on moderate-to-low TYLCD incidence and severity, and superior yield among the evaluated tomato cultivars. Therefore, identifying the most resistant/tolerant and environmentally suitable cultivars is needed to mitigate the viral disease in tomatoes.

PMID:40857747 | DOI:10.1094/PDIS-03-25-0469-RE

New Phytol. 2025 Aug 20. doi: 10.1111/nph.70468. Online ahead of print.

ABSTRACT

Herbaceous plant species have been the focus of extensive, long-term research into climate change responses, but there has been little effort to synthesize results and predicted outlooks. This primer summarizes research on climate change responses for eight intensively studied herbaceous plant species. We establish generalities across species, examine limitations, and propose a path forward. Climate change has reduced fitness, caused maladaptation, and/or led to population declines in at least part of the range of all six forb species. Plasticity alone is likely not sufficient to allow adjustment to shifting climates. Most model species also have spatially restricted dispersal that may limit genetic and evolutionary rescue. These results are surprising, given that these species are generally widespread, span large elevation ranges, and have substantial genetic and phenotypic variation. The focal species have diverse life histories, reproductive strategies, and habitats, and most are native to North America. Thus, species that are rare, habitat specialists, or endemic to other parts of the world are poorly represented in this review. We encourage researchers to design demographic and field experiments that evaluate plant traits and fitness in contemporary and potential future conditions across the full life cycle, and that consider biotic interactions in climate change responses.

PMID:40836613 | DOI:10.1111/nph.70468

Plant J. 2025 Aug;123(4):e70426. doi: 10.1111/tpj.70426.

ABSTRACT

Solanum verrucosum Schlechtendal (2x = 2n = 24) is unique among the clade 4 Solanum Sect Petota species. In addition to being one of the only fully self-compatible diploid potato species, S. verrucosum is the only clade 4 species that lacks prezygotic interspecific reproductive barriers. This allows S. verrucosum to accept pollen from a broad range of Solanum species and thereby serving as a genetic “bridge” between the cultivated or primary potato gene pool and distantly related wild relatives in the tertiary gene pool. The genetic mechanisms underlying self-compatibility in Solanum often underpin interspecific compatibility interactions, which in S. verrucosum, has been attributed to the lack of S-RNase expression. Using an interspecific F2 mapping population (n = 150), we investigated the genetic mechanisms responsible for the lack of interspecific reproductive barriers in S. verrucosum. This F2 population was evaluated for the ability to accept pollen from two clade 1, 1 EBN species (S. pinnatisectum and S. tarnii); from which two QTL for interspecific compatibility were identified on chromosomes 1 and 11, explaining 56.6% of the phenotypic variation observed. To identify the genetic basis of interspecific compatibility, we generated a chromosome-scale genome assembly of S. verrucosum MSII1813-2 and performed gene expression profiling of reproductive organs. Differential gene expression of S-RNase, located within the chromosome 1 QTL, confirmed the central role of the S-locus and specifically, S-RNase, in interspecific compatibility. Discovery of a non-S-locus QTL is consistent with previous findings that other non-S-locus factors are necessary for interspecific compatibility in S. verrucosum.

PMID:40836693 | DOI:10.1111/tpj.70426

China CDC Wkly. 2025 Aug 1;7(31):1031-1037. doi: 10.46234/ccdcw2025.175.

ABSTRACT

WHAT IS ALREADY KNOWN ABOUT THIS TOPIC?: Chronic diseases and multimorbidity impose substantial burdens on healthcare systems globally, particularly in aging populations, resulting in elevated healthcare utilization rates and increased expenditures.

WHAT IS ADDED BY THIS REPORT?: This study validates previous research findings using an extensive administrative database from a major city in South China. Additionally, it provides comprehensive estimates of annual hospitalization expenditures per patient associated with chronic diseases and multimorbidity patterns among older adults, elucidating the economic burden and cost variations across specific diseases and multimorbidity combinations. Cancer, cerebrovascular disease (CVD), and heart disease – whether occurring individually or in conjunction with other chronic conditions, particularly within complex multimorbidity patterns – were associated with substantial annual hospitalization expenditures and significant healthcare resource utilization.

WHAT ARE THE IMPLICATIONS FOR PUBLIC HEALTH PRACTICE?: Disease burden studies provide critical evidence for prioritizing public health policies and targeted interventions. Policymakers should implement comprehensive prevention strategies, evidence-based interventions, appropriate reimbursement policies, and integrated management approaches to control disease progression and reduce healthcare expenditures.

PMID:40831617 | PMC:PMC12360313 | DOI:10.46234/ccdcw2025.175

Proc Natl Acad Sci U S A. 2025 Aug 26;122(34):e2503491122. doi: 10.1073/pnas.2503491122. Epub 2025 Aug 20.

ABSTRACT

The chemical composition of wood plays a pivotal role in the adaptability and structural integrity of trees. However, few studies have investigated the environmental factors that determine lignin composition and its biological significance in plants. Here, we examined the lignin syringyl-to-guaiacyl (S/G) ratio in members of a Populus trichocarpa population sourced from their native habitat and conducted a genome wide association study to identify genes linked to lignin formation. Our results revealed many significant associations, suggesting that lignin biosynthesis is a complex polygenic trait. Additionally, we found an increase in the S/G ratio from northern to southern geographic origin of the trees sampled, along with a corresponding metabolic and transcriptional reprogramming of xylem cell wall biosynthesis. Further molecular analysis identified a mutation in a cell wall laccase genetically associated with higher S/G ratios that predominate in trees from warmer lower latitudes. Collectively, our findings suggest that lignin heterogeneity arises from an evolutionary process enabling poplar adaptation to different climatic challenges.

PMID:40833412 | DOI:10.1073/pnas.2503491122

Nat Plants. 2025 Aug 8. doi: 10.1038/s41477-025-02079-6. Online ahead of print.

ABSTRACT

The hexaploid sweetpotato (Ipomoea batatas [L.] Lam.) is a globally important stable crop that plays a key role in biofortification. Its high resilience and adaptability provide distinct advantages in addressing food security and climate challenges. Here we report a haplotype-resolved chromosome-level genome assembly of an African cultivar, ‘Tanzania’, revealing mosaic genomic origins along haplotype-phased chromosomes. The wild tetraploid I. aequatoriensis, currently found in coastal Ecuador, contributes to a substantial fraction of the sweetpotato genome. Another large proportion of the genome shows a closer genetic relationship to the wild tetraploid I. batatas 4×, distributed in Central America. The sequences contributed by different wild species are not distributed in typical subgenomes but are intertwined along chromosomes, possibly owing to the known non-preferential recombination among sweetpotato haplotypes. This study improves our understanding of sweetpotato origin and genome architecture and provides valuable genomic resources to accelerate sweetpotato breeding.

PMID:40781486 | DOI:10.1038/s41477-025-02079-6

Sci Data. 2025 Aug 5;12(1):1362. doi: 10.1038/s41597-025-05131-4.

ABSTRACT

Biological nitrogen fixation (BNF) is the main natural source of new nitrogen inputs in terrestrial ecosystems, supporting terrestrial productivity, carbon uptake, and other Earth system processes. We assembled a comprehensive global dataset of field measurements of BNF in all major N-fixing niches across natural terrestrial biomes derived from the analysis of 376 BNF studies. The dataset comprises 32 variables, including site location, biome type, N-fixing niche, sampling year, quantification method, BNF rate (kg N ha^-1 y^-1), the percentage of nitrogen derived from the atmosphere (%N_dfa), N fixer or N-fixing substrate abundance, BNF rate per unit of N fixer abundance, and species identity. Overall, the dataset combines 1,207 BNF rates for trees, shrubs, herbs, soil, leaf litter, woody litter, dead wood, mosses, lichens, and biocrusts, 152 herb %N_dfa values, 1,005 measurements of N fixer or N-fixing substrate abundance, and 762 BNF rates per unit of N fixer abundance for a total of 424 species across 66 countries. This dataset facilitates synthesis, meta-analysis, upscaling, and model benchmarking of BNF fluxes at multiple spatial scales.

PMID:40764484 | DOI:10.1038/s41597-025-05131-4

Plant Dis. 2025 Aug 6. doi: 10.1094/PDIS-12-24-2589-SR. Online ahead of print.

ABSTRACT

Gummy stem blight (GSB), caused by three Stagonosporopsis species, S. citrulli, S. cucurbitacearum and S. caricae, is one of the most economically important diseases hindering watermelon production worldwide. Since there is no commercial resistance to GSB in watermelon cultivars, its management depends on cultural practices and preventative fungicides. Therefore, efficient methods for the detection of Stagonosporopsis species that could aid management decisions are required. To help achieve this, a loop-mediated isothermal amplification (LAMP) assay specific to S. citrulli (SCIT850) was developed under two detection formats: fluorescence quantification and endpoint colorimetric detection. The SCIT850 assay was determined to be specific to its target species and exhibited a consistent sensitivity of 1 pg of genomic DNA under both formats. The assay can be combined with a previously reported LAMP assay for the collective detection of the three Stagonosporopsis spp. (STAGY), which have comparable sensitivity to SCIT850 and can aid in species discrimination. A field diagnostic system for GSB-causing Stagonosporopsis was developed by coupling the SCIT850 and STAGY assays to quick DNA extraction protocols. Two DNA extraction methods were tested: one from leaves using cellulose dipsticks, and one from steel rods (typical of spore traps) using Chelex100. With the dipstick method, we detected pathogen DNA in inoculated asymptomatic, mildly infected, and severely infected plants, while with the Chelex100 we detected pathogen DNA from rods infested with as few as 500 spores. The SCIT850 and STAGY assays coupled with these quick sample processing methods could be adapted for field deployment, which would allow growers to make efficient and timely management decisions based on detection of the actual Stagonosporopsis species present in the field.

PMID:40767855 | DOI:10.1094/PDIS-12-24-2589-SR

Proc Natl Acad Sci U S A. 2025 Aug 12;122(32):e2426650122. doi: 10.1073/pnas.2426650122. Epub 2025 Aug 6.

ABSTRACT

Cells accumulate mutations throughout development, contributing to cancer, aging, and evolution. Quantitative data on the abundance of de novo mutations within plants or animals are limited, as new mutations are often rare within a tissue and fall below the limits of current sequencing depths and error rates. Here, we show that mutations induced by the maize Mutator (Mu) transposon can be reliably quantified down to a detection limit of 1 part in 16,000. We measured the abundance of millions of de novo Mu insertions across four tissue types. Within a tissue, the distribution of de novo Mu allele frequencies was highly reproducible between plants, showing that, despite the stochastic nature of mutation, repeated statistical patterns of mutation abundance emerge. In contrast, there were significant differences in the allele frequency distribution between tissues. At the extremes, root was dominated by a small number of highly abundant de novo insertions, while endosperm was characterized by thousands of insertions at low allele frequencies. Finally, we used the measured pollen allele frequencies to reinterpret a classic genetic experiment, showing that evidence for late Mu activity in pollen is better explained by cell division statistics. These results provide insight into the complexity of mutation accumulation in multicellular organisms and a system to interrogate the factors that shape mutation abundance.

PMID:40768352 | DOI:10.1073/pnas.2426650122

BMC Microbiol. 2025 Jul 28;25(1):456. doi: 10.1186/s12866-025-04175-1.

ABSTRACT

BACKGROUND: The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates.

RESULTS: Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110 bp and at 370 bp, while strains only displaying the 110 bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification.

CONCLUSIONS: The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.

PMID:40722002 | DOI:10.1186/s12866-025-04175-1

Insects. 2025 Jun 24;16(7):653. doi: 10.3390/insects16070653.

ABSTRACT

Blueberry is a high-value fruit crop in the United States, with Georgia and Florida serving as important early-season production regions. In these areas, several thrips species (Thysanoptera: Thripidae), including Frankliniella tritici (Fitch), Frankliniella bispinosa (Morgan), and Scirtothrips dorsalis (Hood), have emerged as economically significant pests. While F. tritici and F. bispinosa primarily damage floral tissues, S. dorsalis targets young foliage. Their rapid reproduction, high mobility, and broad host range contribute to rapid population buildup and complicate the management programs. Species identification is often difficult due to overlapping morphological features and requires the use of molecular diagnostic tools for accurate identification. Although action thresholds, such as 2-6 F. tritici per flower cluster, are used to guide management decisions, robust economic thresholds based on yield loss remain undeveloped. Integrated pest management (IPM) practices include regular monitoring, cultural control (e.g., pruning, reflective mulch), biological control using Orius insidiosus (Say) and predatory mites, and chemical control. Reduced-risk insecticides like spinetoram and spinosad offer effective suppression while minimizing harm to pollinators and beneficial insects. However, the brief flowering period limits the establishment of biological control agents. Developing species-specific economic thresholds and phenology-based IPM strategies is critical for effective and sustainable thrips management in blueberry cropping systems.

PMID:40725285 | DOI:10.3390/insects16070653

Plant Sci. 2025 Jul 23:112682. doi: 10.1016/j.plantsci.2025.112682. Online ahead of print.

ABSTRACT

Enhanced protein degradation, typically conducted by the coordinated action of proteases and the ubiquitin-proteasome system (UPS), is a common response to heat stress. It works by removing nonfunctional or damaged proteins to maintain normal cell function and to allow for the remobilization of nutrients, enabling plants to respond rapidly to environmental perturbation. Despite its crucial role, there has been limited research addressing proteolysis activities from both proteases and the UPS in grasses exposed to heat stress. This project aims to quantify activities of proteases and the UPS in different lines of creeping bentgrass (Agrostis stolonifera L.), a cool-season turfgrass that’s prized for its functional and aesthetic qualities, and detect changes in expression levels of known proteases and the UPS genes. Previously identified heat-tolerant and -sensitive creeping bentgrass lines were selected for this study. They were exposed to either control (20/15°C day/night) or heat stress (38/33°C day/night) treatments for 35 d. Protein degradation was enhanced under heat as demonstrated by significant increases in protease activity and the UPS activity over time. A more heat-tolerant line, S11 729-10, maintained lower activities of both protease and the UPS, contributing to its higher protein contents, and thereby greater thermotolerance. Additionally, gene expression was variable across lines, with heat sensitive Crenshaw having lower expression levels as heat stress progressed. This is the first time that the roles of protease activity and the UPS activity in heat stress were simultaneously analyzed in a perennial grass species. Such information will broaden the understanding of how protein degradation is regulated in response to heat stress, providing a deeper insight into thermotolerance mechanisms in creeping bentgrass.

PMID:40712792 | DOI:10.1016/j.plantsci.2025.112682

Front Plant Sci. 2025 Jul 11;16:1607733. doi: 10.3389/fpls.2025.1607733. eCollection 2025.

ABSTRACT

Maize (Zea mays L.) is the most widely produced crop in the world, and conventional production requires significant amounts of synthetic nitrogen fertilizer, which has negative economic and environmental consequences. Maize landraces from Oaxaca, Mexico, can acquire nitrogen from nitrogen-fixing bacteria that live in a mucilage secreted by aerial nodal roots. The development of these nodal roots is a characteristic traditionally associated with the juvenile vegetative stage of maize plants. However, mature Oaxacan landraces develop many more nodes with aerial roots than commercial maize varieties. Our study shows that Oaxacan landraces develop aerial roots during the juvenile and adult vegetative phases and even during early flowering under greenhouse and field conditions. Surprisingly, the development of these roots was only minimally affected by soil nitrogen and ambient humidity. These findings are an essential first step in developing maize varieties to reduce fertilizer needs in maize production across different environmental conditions.

PMID:40718026 | PMC:PMC12289584 | DOI:10.3389/fpls.2025.1607733

Fungal Biol. 2025 Aug;129(5):101590. doi: 10.1016/j.funbio.2025.101590. Epub 2025 May 6.

ABSTRACT

The Fifth International Symposium on Fungal Stress (ISFUS) brought together in Brazil many of the leaders in the field of fungal stress responses, from fourteen countries, for four days of outstanding science ranging from basic research to studies with agricultural, medical, industrial, and environmental significance. In addition to the excellent oral and poster presentations, the Symposium organisers ensured that all participants had ample opportunity to engage, socialise, and network to exchange ideas and share research. The conference was enhanced by the world-class venue near Iguazu Falls, probably the greatest natural phenomenon in South America.

PMID:40707112 | DOI:10.1016/j.funbio.2025.101590

Mol Ecol Resour. 2025 Jul 22:e70012. doi: 10.1111/1755-0998.70012. Online ahead of print.

ABSTRACT

Yellow monkeyflowers (Mimulus guttatus complex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan-genomics in this group, we present four chromosome-scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a single M. guttatus population, one from the closely related selfing species M. nasutus, and one from a more divergent species M. tilingii. All assemblies are highly complete and resolve centromeric and repetitive regions. Comparative analyses reveal such extensive structural variation in repeat-rich, gene-poor regions that large portions of the genome are unalignable across accessions. As a result, this Mimulus pan-genome is primarily informative in genic regions, underscoring limitations of resequencing approaches in such polymorphic taxa. We document gene presence-absence, investigate the recombination landscape using high-resolution linkage data, and quantify nucleotide diversity. Surprisingly, pairwise differences at fourfold synonymous sites are exceptionally high-even in regions of very low recombination-reaching ~3.2% within a single M. guttatus population, ~7% within the interfertile M. guttatus species complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolated M. tilingii. Genome-wide patterns of nucleotide variation show little evidence of linked selection, and instead suggest that the concentration of genes (and likely selected sites) in high-recombination regions may buffer diversity loss. These assemblies, annotations, and comparative analyses provide a robust genomic foundation for Mimulus research and offer new insights into the interplay of recombination, structural variation, and molecular evolution in highly diverse plant genomes.

PMID:40693537 | DOI:10.1111/1755-0998.70012

Plant Physiol. 2025 Jul 3;198(3):kiaf294. doi: 10.1093/plphys/kiaf294.

ABSTRACT

Minimal native and synthetic Polymerase III promoters enable efficient and customizable CRISPR multiplexing in plants, expanding genome engineering capabilities

PMID:40673482 | PMC:PMC12268498 | DOI:10.1093/plphys/kiaf294

Nature. 2025 Jul;643(8072):705-711. doi: 10.1038/s41586-025-09201-w. Epub 2025 Jul 16.

ABSTRACT

Biological nitrogen fixation (BNF) is the largest natural source of new nitrogen (N) that supports terrestrial productivity^1,2, yet estimates of global terrestrial BNF remain highly uncertain^3,4. Here we show that this uncertainty is partly because of sampling bias, as field BNF measurements in natural terrestrial ecosystems occur where N fixers are 17 times more prevalent than their mean abundances worldwide. To correct this bias, we develop new estimates of global terrestrial BNF by upscaling field BNF measurements using spatially explicit abundances of all major biogeochemical N-fixing niches. We find that natural biomes sustain lower BNF, 65 (52-77) Tg N yr^-1, than previous empirical bottom-up estimates^3,4, with most BNF occurring in tropical forests and drylands. We also find high agricultural BNF in croplands and cultivated pastures, 56 (54-58) Tg N yr^-1. Agricultural BNF has increased terrestrial BNF by 64% and total terrestrial N inputs from all sources by 60% over pre-industrial levels. Our results indicate that BNF may impose stronger constraints on the carbon sink in natural terrestrial biomes and represent a larger source of agricultural N than is generally considered in analyses of the global N cycle^5,6, with implications for proposed safe operating limits for N use^7,8.

PMID:40670639 | DOI:10.1038/s41586-025-09201-w

Nat Chem Biol. 2025 Jul 16. doi: 10.1038/s41589-025-01970-9. Online ahead of print.

ABSTRACT

Monoterpene indole alkaloids (MIAs) are a large, structurally diverse class of bioactive natural products. These compounds are biosynthetically derived from a stereoselective Pictet-Spengler condensation that generates a tetrahydro-β-carboline scaffold characterized by a 3S stereocenter. However, a subset of MIAs contains a noncanonical 3R stereocenter. Here we report the basis for 3R-MIA biosynthesis in Mitragyna speciosa (kratom). We discover the presence of the iminium species (20S)-3-dehydrocorynantheidine, which supports isomerization of 3S to 3R via oxidation and stereoselective reduction downstream of the initial Pictet-Spengler condensation. Isotopologue feeding experiments identify the sites for downstream MIA pathway biosynthesis as well as the oxidase/reductase pair that catalyzes this epimerization. This oxidase/reductase pair has broad substrate specificity, suggesting that this pathway may be responsible for the formation of many 3R-MIAs and downstream spirooxindole alkaloids in kratom. The elucidation of this epimerization mechanism allows biocatalytic access to a range of pharmacologically active spirooxindole alkaloid compounds.

PMID:40670688 | DOI:10.1038/s41589-025-01970-9

Mol Ecol. 2025 Jul 17:e70033. doi: 10.1111/mec.70033. Online ahead of print.

ABSTRACT

Endemic pathogens continue to pose threats of recurring outbreaks, especially in agricultural settings. How these outbreaks unfold and what drives the variability in disease epidemics is less understood. We addressed this question in the Xanthomonas-tomato pathosystem by developing an integrated approach that linked the within-field quantitative signature of local pathogen diversity to climatic conditions to explain variable bacterial disease epidemics across fields. Using strain-resolved metagenomics, we found that pathogen heterogeneity with multiple co-occurring lineages is common. Higher disease severity was associated with higher pathogen diversity. Considering these observations, we used response-specific regression models to investigate the role of environmental variables in driving differences in disease and strain dynamics. Abrupt and frequent changes in environmental factors explained the variability of disease severity. We observed variable lineage dynamics across fields, but at least two lineages with divergent, climate-dependent fitness strategies coexisted throughout the growing season without either of them taking the lead. We further profiled the dynamics of single-nucleotide polymorphism variants in the pathogen population and observed that some alleles are temporarily favoured by specific climatic conditions encountered throughout the growing season, leading to oscillating seasonal patterns of allelic frequencies. These alleles can be referred to as seasonal alleles. Overall, our study revealed that the seasonal fluctuations in pathogen strain composition, diversity and climate-influenced pathogen fitness play a significant role in shaping the severity and variability of bacterial spot disease outbreaks.

PMID:40673408 | DOI:10.1111/mec.70033

Plant J. 2025 Jul;123(2):e70294. doi: 10.1111/tpj.70294.

ABSTRACT

Advances in engineering of bioenergy crops were driven over the past years by adapting technological breakthroughs and accelerating conventional applications but also exposed intriguing challenges. New tools revealed rich interconnectivity in the exponentially growing and dynamic ‘big’ omics data’ of metabolomes, transcriptomes, and genomes at previously inaccessible magnitude (global, cross-species, meta-) and resolution (single cell). Insights enabled fresh hypotheses and stimulated disciplines such as functional genomics with discovery of broad regulatory networks and their determinants, that is, DNA parts, including promoters, regulatory elements, and transcription factors. Their rational design, assembly into increasingly complex blueprints, and installation into diverse chassis is an existing frontier that may benefit from emerging technologies to address bottlenecks. Interweaving nature-inspired to fully synthetic parts has already allowed building of fine-tuned regulatory circuits, or new-to-nature metabolic routes insulated from the biological context of the chassis species. Similarly, developments and the evolving need for unifying principles in plant transformation and species-agnostic technologies highlight future opportunities for engineering the next generation of bioenergy plants.

PMID:40674648 | DOI:10.1111/tpj.70294

PLoS Genet. 2025 Jul 16;21(7):e1011742. doi: 10.1371/journal.pgen.1011742. Online ahead of print.

ABSTRACT

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used genotype-by-sequencing data to score more than 10,000 maize and teosinte lines for the presence or absence of each driver. Fewer than ~0.5% of modern inbred lines carry chromosomal drivers. In contrast, among individuals from 5331 open-pollinated landraces, 6.32% carried Ab10, 5.16% carried K10L2, and 12.28% carried at least one B chromosome. These frequencies are consistent with those reported in previous studies. Using a GWAS approach we identified unlinked loci that associate with the presence or absence of the selfish genetic elements. Many significant SNPs are positively associated with the drivers, suggesting that there may have been selection for alleles that ameliorate their negative fitness consequences. We then assessed the contributions of population structure, associated loci, and the environment on the distribution of each chromosomal driver. There was no significant relationship between any chromosomal driver and altitude, contrary to conclusions based on smaller studies. Our data suggest that the distribution of the major chromosomal drivers is primarily influenced by neutral processes and the deleterious fitness consequences of the drivers themselves. While each driver has a unique relationship to genetic background and the environment, they are largely unconstrained by either.

PMID:40668866 | DOI:10.1371/journal.pgen.1011742

Front Plant Sci. 2025 Jun 30;16:1588485. doi: 10.3389/fpls.2025.1588485. eCollection 2025.

ABSTRACT

Pearl millet [Cenchrus americanus (L.) Morrone, formerly Pennisetum glaucum (L.) R. Br.] is the sixth most important cereal globally and is used for forage and feed in the U.S. To identify genomic regions governing important physiological, agronomic and yield related traits, a recombinant inbred line population derived from the cross between Tift 99D₂B_{1 ×} Tift 454 was phenotyped in the field in 2006, 2007 and 2013. In addition, the population was phenotyped for root-knot nematode resistance in the greenhouse during 2009. Using a previously generated genetic map containing 505 single nucleotide polymorphism markers and composite interval mapping, we identified 45 QTLs for eight traits (plant height, stem diameter, days to heading, panicle diameter, panicle length, 1000 seed weight, Pyricularia leaf spot disease, and root-knot nematode egg mass) across almost all linkage groups. These QTLs explained 6.31 to 32.51% of phenotypic variance for each trait and were consistently detected over different environments. Plant height and days to heading were colocalized on LG2 and LG5 showing maturity and plant height are linked and influence each other, similarly to other cereal crops. Interestingly, 5 of 19 QTLs linked to plant height, stem diameter, panicle diameter, and panicle length colocalized to the same locations on LG3, indicating breeding for one trait could simultaneously improve the other. The markers and genes identified in the present study can be used in developing high yielding pearl millet varieties using marker-assisted selection.

PMID:40661761 | PMC:PMC12256767 | DOI:10.3389/fpls.2025.1588485

Mol Ecol. 2025 Jul 15:e70024. doi: 10.1111/mec.70024. Online ahead of print.

ABSTRACT

Understanding the impact of domestication on deleterious mutations has fascinated evolutionary biologists and breeders alike. A ‘cost of domestication’ has been reported for some organisms through accumulation of gene disruptions or radical amino acid changes. However, recent evidence paints a more complex picture of this phenomenon in different domesticated species. In this study, we used genomic sequences of 253 tomato accessions to investigate the evolution of deleterious mutations and genomic structural variants (SVs) through tomato domestication history. We apply phylogeny-based methods to identify deleterious mutations in the domesticated tomato as well as its semi-wild and wild relatives. Our results implicate a downward trend throughout domestication in the number of genetic variants, regardless of their functional impact. This suggests that demographic factors have reduced overall genetic diversity, leading to lower deleterious load and SVs as well as loss of some beneficial alleles during tomato domestication. However, we detected an increase in proportions of nonsynonymous and deleterious alleles (relative to synonymous and neutral nonsynonymous alleles, respectively) during the initial stage of tomato domestication in Ecuador. Additionally, deleterious alleles in the commonly cultivated tomato seem to be more frequent than expected under a neutral hypothesis of molecular evolution. Our analyses also revealed frequent deleterious alleles in several well-studied tomato genes, probably involved in response to biotic and abiotic stress as well as fruit development and flavour regulation. To provide a practical guide for breeding experiments, we created TomDel, a public searchable database of 21,162 potentially deleterious alleles identified in this study (hosted on the Solanaceae Genomic Network; https://solgenomics.net/).

PMID:40662302 | DOI:10.1111/mec.70024

Plants (Basel). 2025 Jun 24;14(13):1937. doi: 10.3390/plants14131937.

ABSTRACT

Advances in spinning technology have increased the demand for upland cotton (Gossypium hirsutum L.) cultivars with superior fiber quality. However, progress in breeding for traits such as fiber length is constrained by limited phenotypic and genetic diversity within upland cotton. Introgression from Gossypium barbadense, a closely related species known for its superior fiber traits, offers a promising strategy. Sealand 883 is an obsolete upland germplasm developed through G. barbadense introgression and is known for its long and fine fibers. Previous studies have identified a fiber length quantitative trait locus (QTL) on Chromosome 25, designated qFL–Chr.25, in Sealand 883, conferred by an allele introgressed from G. barbadense. This study evaluated the effect of qFL–Chr.25 in near-isogenic introgression lines (NIILs) using Advanced Fiber Information System (AFIS) measurements. Across four genetic backgrounds, NIILs carrying qFL–Chr.25 consistently exhibited longer fibers, as reflected in multiple length parameters, including UHML, L(n), L(w), UQL(w), and L5%. Newly developed TaqMan SNP diagnostic markers flanking the QTL enable automated, reproducible, and scalable screening of large populations typical in commercial breeding programs. These markers will facilitate the incorporation of qFL–Chr.25 into commercial breeding pipelines, accelerating fiber quality improvement and enhancing the competitiveness of cotton against synthetic fibers.

PMID:40647946 | PMC:PMC12251603 | DOI:10.3390/plants14131937

Plants (Basel). 2025 Jul 7;14(13):2082. doi: 10.3390/plants14132082.

ABSTRACT

Cotton is the most widely cultivated natural fiber crop worldwide, yet it is highly susceptible to various diseases and pests that significantly compromise both yield and quality. To enable rapid and accurate diagnosis of cotton diseases and pests-thus supporting the development of effective control strategies and facilitating genetic breeding research-we propose a lightweight model, the Resource-efficient Cotton Network (RF-Cott-Net), alongside an open-source image dataset, CCDPHD-11, encompassing 11 disease categories. Built upon the MobileViTv2 backbone, RF-Cott-Net integrates an early exit mechanism and quantization-aware training (QAT) to enhance deployment efficiency without sacrificing accuracy. Experimental results on CCDPHD-11 demonstrate that RF-Cott-Net achieves an accuracy of 98.4%, an F1-score of 98.4%, a precision of 98.5%, and a recall of 98.3%. With only 4.9 M parameters, 310 M FLOPs, an inference time of 3.8 ms, and a storage footprint of just 4.8 MB, RF-Cott-Net delivers outstanding accuracy and real-time performance, making it highly suitable for deployment on agricultural edge devices and providing robust support for in-field automated detection of cotton diseases and pests.

PMID:40648091 | PMC:PMC12252015 | DOI:10.3390/plants14132082

Tree Physiol. 2025 Jul 11:tpaf081. doi: 10.1093/treephys/tpaf081. Online ahead of print.

ABSTRACT

The success of CRISPR genome editing studies depends critically on the precision of guide RNA (gRNA) design. Sequence polymorphisms in outcrossing tree species pose design hazards that can render CRISPR genome editing ineffective. Despite recent advances in tree genome sequencing with haplotype resolution, sequence polymorphism information remains largely inaccessible to various functional genomics research efforts. The Populus VariantDB v3.2 addresses these challenges by providing a user-friendly search engine to query sequence polymorphisms of heterozygous genomes. The database accepts short sequences, such as gRNAs and primers, as input for searching against multiple poplar genomes, including hybrids, with customizable parameters. We provide examples to showcase the utilities of VariantDB in improving the precision of gRNA or primer design. The platform-agnostic nature of the probe search design makes Populus VariantDB v3.2 a versatile tool for the rapidly evolving CRISPR field and other sequence-sensitive functional genomics applications. The database schema is expandable and can accommodate additional tree genomes to broaden its user base.

PMID:40643191 | DOI:10.1093/treephys/tpaf081

Tree Physiol. 2025 Jul 11:tpaf080. doi: 10.1093/treephys/tpaf080. Online ahead of print.

ABSTRACT

Sulfate-proton co-transporters (SULTRs) mediate sulfate uptake, transport, storage, and assimilation in plants. The SULTR family has historically been classified into four groups (SULTR1-SULTR4), with well-characterized roles for SULTR groups 1, 2, and 4. However, the functions of the large and diverse SULTR3 group remain poorly understood. Here, we present an updated phylogenetic analysis of SULTRs across angiosperms, including multiple early-divergent lineages. Our results suggest that the enigmatic SULTR3 group comprises four distinct subfamilies that predate the emergence of angiosperms, providing a basis for reclassifying the SULTR family into seven subfamilies. This expanded classification is supported by subfamily-specific gene structures and amino acid substitutions in the substrate-binding pocket. Structural modeling identified three serine residues uniquely lining the substrate-binding pocket of SULTR3.4, enabling three hydrogen bonds with the phosphate ion. The data support the proposed neofunctionalization of this subfamily for phosphate allocation within vascular tissues. Transcriptome analysis of Populus tremula × alba revealed divergent tissue expression preferences among SULTR subfamilies and between genome duplicates. We observed partitioned expression in vascular tissues among the four SULTR3 subfamilies, with PtaSULTR3.4a and PtaSULTR3.2a preferentially expressed in primary and secondary xylem, respectively. Gene coexpression analysis revealed coordinated expression of PtaSULTR3.4a with genes involved in phosphate starvation responses and nutrient transport, consistent with a potential role in phosphate homeostasis. In contrast, PtaSULTR3.2a was strongly coexpressed with lignification and one-carbon metabolism genes and their upstream transcription regulators. PtaSULTR3.2a belongs to a eudicot-specific branch of the SULTR3.1 subfamily found only in perennial species, suggesting a specialized role in lignifying tissues. Together, our findings provide a refined phylogenetic framework for the SULTR family and suggest that the expanded SULTR3 subfamilies have undergone neofunctionalization during the evolution of vascular and perennial plants.

PMID:40643194 | DOI:10.1093/treephys/tpaf080

J Gen Virol. 2025 Jul;106(7). doi: 10.1099/jgv.0.002119.

ABSTRACT

Orthotospovirus tomatomaculae [tomato spotted wilt virus (TSWV)] is a major pathogen in horticultural and row crops worldwide including the USA. In this study, tomato spotted wilt disease incidence was monitored in Arachis hypogaea (peanut; year 1990 to 2024) and Nicotiana tabacum (tobacco; year 2000 to 2024) in commercial farmers’ fields in the Southeastern USA. Furthermore, nucleocapsid (N), nonstructural movement (NSm) and nonstructural silencing suppressor (NSs) protein gene sequences of TSWV global populations from North America, South America, Europe, Asia-Pacific, Africa and Australia were compared with local US population and analysed to understand the genetic variability in the virus genome. In our study, full-length sequences of 94 N, 111 NSm and 78 NSs genes were amplified from TSWV-infected A. hypogaea (peanut), Capsicum annuum (pepper), N. tabacum (tobacco) and Solanum lycopersicum (tomato). nt-based phylogenetic analysis of N, NSm and NSs genes correlated with the geographical location of the TSWV isolates, with notably higher substitution rates in the population of recent years. In addition, the least genetic variability was observed in the N gene of the local population upon comparison with other global TSWV population. The neutrality test of TSWV suggested a non-neutral evolution of the virus genome. Low variation among the selected genes might be attributed to strong purifying selection pressure in the populations. Furthermore, estimation of selection pressure (dN/dS) on small (S) segment-encoded N protein and nonstructural protein showed higher purifying selection than the movement protein encoded by the medium (M) segment of the TSWV isolates. Single-likelihood ancestor counting suggested an overall negative selection pressure on several codons of the selected genes, which indicated that natural selection and population bottleneck events might have influenced the evolution of TSWV. Our study also deciphered high gene flow and low genetic differentiation amid the different TSWV population sets. Additionally, BEAST analysis of TSWV N gene sequences from GA predicted the most common recent ancestor existed ~25 years ago. This data was further correlated with disease incidence data from peanut and tobacco crops obtained in the last three decades. These findings suggest the intermixing of TSWV isolates between peanut, pepper, tobacco and tomato crops, while the virus genome has undergone strong purifying selection.

PMID:40622855 | DOI:10.1099/jgv.0.002119

Plant J. 2025 Jul;123(1):e70304. doi: 10.1111/tpj.70304.

ABSTRACT

Targeted demethylation by DNA glycosylases (DNGs) results in differential methylation between parental alleles in the endosperm, which drives imprinted expression. Here, we performed RNA sequencing on endosperm derived from DNG mutant mdr1 and wild-type (WT) endosperm. Consistent with the role of DNA methylation in gene silencing, we find 108 genes and 96 TEs differentially expressed (DE) transcripts that lost expression in the hypermethylated mdr1 mutant. Compared with other endosperm transcripts, the mdr1 targets are enriched for TEs (particularly Helitrons), and DE genes are depleted for both core genes and GO term assignments, suggesting that the majority of DE transcripts are TEs and pseudo-genes. By comparing DE genes to imprinting calls from prior studies, we find that the majority of DE genes have maternally biased expression, and approximately half of all maternally expressed genes (MEGs) are DE in this study. In contrast, no paternally expressed genes (PEGs) are DE. DNG-dependent imprinted genes are distinguished by maternal demethylation and expression primarily in the endosperm, so we also performed Enzymatic Methyl-seq on hybrids to identify maternal demethylation and utilized a W22 gene expression atlas to identify genes expressed primarily in the endosperm. Overall, approximately ⅔ of all MEGs show evidence of regulation by DNGs. Taken together, this study solidifies the role of MDR1 in the regulation of maternally expressed, imprinted genes and TEs and identifies subsets of genes with DNG-independent imprinting regulation.

PMID:40587880 | DOI:10.1111/tpj.70304

BioTech (Basel). 2025 Jun 12;14(2):48. doi: 10.3390/biotech14020048.

ABSTRACT

Interspecific and intersectional crosses have introduced valuable genetic traits for blueberry (Vaccinium sect. Cyanococcus) cultivar improvement. Introgression from Vaccinium species at the diploid, tetraploid, and hexaploid levels has been found in cultivated blueberries. Continued efforts to integrate wild blueberry genetic resources into blueberry breeding are essential to broaden the genetic diversity of cultivated blueberries. However, performing heteroploid crosses among Vaccinium species is challenging. Polyploid induction through tissue culture has been useful in bridging ploidy barriers. Mixoploid or chimeric shoots often are produced, along with solid polyploid mutants. These chimeras are mostly discarded because of their genome instability and the difficulty in identifying periclinal mutants carrying germline mutations. Since induced polyploidy in blueberries often results in a low frequency of solid mutant lines, it is important to recover solid polyploids through chimera dissociation. In this study, two vegetative propagation methods, i.e., axillary and adventitious shoot induction, were evaluated for their efficiency in chimera dissociation. Significantly higher rates of chimera dissociation were found in adventitious shoot induction compared to axillary shoot induction. Approximately 89% and 82% of the adventitious shoots induced from mixoploid lines 145.11 and 169.40 were solid polyploids, respectively, whereas only 25% and 53% of solid polyploids were recovered through axillary shoot induction in these lines. Effective chimera dissociation provides useful and stable genetic materials to enhance blueberry breeding.

PMID:40558397 | DOI:10.3390/biotech14020048

bioRxiv [Preprint]. 2025 May 28:2025.05.23.655667. doi: 10.1101/2025.05.23.655667.

ABSTRACT

Repairing a damaged body part is critical for the survival of any organism. In plants, tissue damage induces rapid responses that activate defense, regeneration and wound healing. While early wound signaling mediated by phytohormones, electrical signals and reactive oxygen species is well-characterized, the mechanisms governing the final stages of wound healing remain poorly understood. Here, we show that wounding in Arabidopsis leaves induces localized cooling, likely due to evaporative water loss, accompanied by the activation of cold-responsive genes. The subsequent disappearance of localized cooling and deactivation of cold-responsive genes serve as a quantitative marker of wound healing. Based on these observations, we developed a workflow by leveraging computer vision and deep learning to monitor the dynamics of wound healing. We found that CBFs transcription factors relay injury-induced cooling signal to wound healing. Thus, our work advances our understanding of tissue repair and provides a tool to quantify wound healing in plants.

PMID:40502075 | PMC:PMC12154623 | DOI:10.1101/2025.05.23.655667

Phytopathology. 2025 Jun 22. doi: 10.1094/PHYTO-03-25-0093-R. Online ahead of print.

ABSTRACT

Phony peach disease (PPD), caused by Xylella fastidiosa subsp. multiplex (Xfm), poses a significant threat to commercial peach orchards in Georgia. Early and accurate detection is essential for effective disease management, yet visual assessment remains the primary approach for diagnosing PPD symptoms due to the high cost and logistical challenges of qPCR-based detection of Xfm. We evaluated the accuracy of visual PPD assessment and examined the factors influencing rater performance, symptom reliability, and optimal survey deployment strategies with CART/Random Forest analyses and simulations. Internode length was the most reliable symptom for PPD identification in two peach cultivars, consistently outperforming other physical traits such as canopy flatness and shape. Primer pair C06Xf-bamA had the greatest relative sensitivity, making it the preferred choice for qPCR confirmation. Principal component analysis suggested that rater experience significantly improved agreement with qPCR results and repeated assessments of the same orchards further enhanced consistency for raters. Simulations results suggested that deploying two experienced raters may provide the highest detection diagnostic accuracy for survey purposes, particularly when qPCR-based pathogen detection is unavailable. Last, PPD-affected trees, through PCR verification and visual identification, exhibited higher mortality rates than Xfm-negative trees, reinforcing the need for early detection and removal to limit disease spread. These findings underscore the importance of strategic rater deployment, targeted symptom selection, and integrating molecular diagnostics when feasible.

PMID:40544457 | DOI:10.1094/PHYTO-03-25-0093-R

bioRxiv [Preprint]. 2025 May 27:2025.05.22.655462. doi: 10.1101/2025.05.22.655462.

ABSTRACT

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used genotype-by-sequencing data to score more than 10,000 maize and teosinte lines for the presence or absence of each driver. Less than ~0.5% of modern inbred lines carry chromosomal drivers. Among individuals from 5331 open-pollinated landraces, 6.32% carried Ab10, 5.16% carried K10L2, and 12.28% carried at least one B chromosome. Using a GWAS approach we identified unlinked loci that associate with the presence or absence of the selfish genetic elements. Many genetic modifiers are positively associated with the drivers, suggesting that there may have been selection for alleles that ameliorate their negative fitness consequences. We then assessed the contributions of population structure, associated loci, and the environment on the distribution of each chromosomal driver. There was no significant relationship between any chromosomal driver and altitude, contrary to conclusions based on smaller studies. Our data suggest that the distribution of the major chromosomal drivers is primarily influenced by neutral processes and the deleterious fitness consequences of the drivers themselves. While each driver has a unique relationship to genetic background and the environment, they are largely unconstrained by either.

PMID:40501570 | PMC:PMC12154789 | DOI:10.1101/2025.05.22.655462

Mol Plant Pathol. 2025 Jun;26(6):e70107. doi: 10.1111/mpp.70107.

ABSTRACT

Acidovorax citrulli, the causal pathogen of bacterial fruit blotch of cucurbits, relies on a functional type III secretion system (T3SS) for pathogenicity. Two-component systems (TCSs) are primary signal transduction mechanisms for bacteria to detect and adapt to various environmental conditions. However, the role of TCS on regulating T3SS and other virulence factors in response to environmental stimuli is still poorly understood in A. citrulli. Here, we report the identification of a conserved TCS, OmpR/EnvZ, involved in hypersensitive response (HR) induction in Nicotiana benthamiana by screening a transposon-insertion library in the group II strain xjL12 of A. citrulli. Transcription analysis confirmed that OmpR_Ac/EnvZ_Ac was upregulated in response to elevated osmotic pressure, low and high pH conditions, and host environment. Deletions of envZ_Ac, ompR_Ac, or both envZ_Ac and ompR_Ac in A. citrulli attenuated virulence to melon seedlings and mature leaf tissues, and delayed HR in N. benthamiana. OmpR_Ac was activated by EnvZ_Ac and directly bound to the promoter region of hrpG, a major regulator of T3SS. This binding activated hrpG transcription and promoted T3SS assembly in T3SS-inducing medium, XVM2. Additionally, the OmpR_Ac/EnvZ_Ac mutants of A. citrulli displayed reduced swimming motility due to impaired flagella formation, but also had enhanced biofilm formation and exopolysaccharide production. OmpR_Ac/EnvZ_Ac regulation of these virulence factors in A. citrulli depended on its own conserved phosphorylation sites. This work illuminates a signalling pathway for regulating the T3SS and provides insights into the OmpR/EnvZ-mediated virulence regulatory network in A. citrulli.

PMID:40524436 | DOI:10.1111/mpp.70107

mSphere. 2025 Jun 17:e0002325. doi: 10.1128/msphere.00023-25. Online ahead of print.

ABSTRACT

Allicin tolerance (alt) clusters in phytopathogenic bacteria, which provide resistance to thiosulfinates like allicin, are challenging to find using conventional approaches due to their varied architecture and the paradox of being vertically maintained within genera despite likely being horizontally transferred. This results in significant sequential diversity that further complicates their identification. Natural language processing (NLP), like techniques such as those used in DeepBGC, offers a promising solution by treating gene clusters like a language, allowing for identifying and collecting gene clusters based on patterns and relationships within the sequences. We curated and validated alt-like clusters in Pantoea ananatis 97-1R, Burkholderia gladioli pv. gladioli FDAARGOS 389, and Pseudomonas syringae pv. tomato DC3000. Leveraging sequences from the RefSeq bacterial database, we conducted comparative analyses of gene synteny, gene/protein sequences, protein structures, and predicted protein interactions. This approach enabled the discovery of several novel alt-like clusters previously undetectable by other methods, which were further validated experimentally. Our work highlights the effectiveness of NLP-like techniques for identifying underrepresented gene clusters and expands our understanding of the diversity and utility of alt-like clusters in diverse bacterial genera. This work demonstrates the potential of these techniques to simplify the identification process and enhance the applicability of biological data in real-world scenarios.IMPORTANCEThiosulfinates, like allicin, are potent antifeedants and antimicrobials produced by Allium species and pose a challenge for phytopathogenic bacteria. Phytopathogenic bacteria have been shown to utilize an allicin tolerance (alt) gene cluster to circumvent this host response, leading to economically significant yield losses. Due to the complexity of mining these clusters, we applied techniques akin to natural language processing to analyze Pfam domains and gene proximity. This approach led to the identification of novel alt-like gene clusters, showcasing the potential of artificial intelligence to reveal elusive and underrepresented genetic clusters and enhance our understanding of their diversity and role across various bacterial genera.

PMID:40525872 | DOI:10.1128/msphere.00023-25

Trends Ecol Evol. 2025 Jun 13:S0169-5347(25)00132-6. doi: 10.1016/j.tree.2025.05.001. Online ahead of print.

ABSTRACT

The resilience of ecosystems to climate disruption requires internal feedbacks that support the stability of ecosystem structure and function. Such feedbacks may include sustained interactions between plants and soil [plant-soil feedback (PSF)]. Theoretically, PSF could either boost or degrade ecosystem resilience. Three criteria must be met to attribute resilience to PSF: (i) The presence or amount of PSF must be manipulated; (ii) the ecosystem must face climate disruption after PSF is manipulated; and (iii) PSF must alter the resistance or recovery of ecosystem structure or function to disruption. Several case studies suggest that PSF may support (or degrade) resilience, but no study has yet met all criteria. Doing so could yield novel insights into how aboveground-belowground interactions shape ecosystem resilience to climate change.

PMID:40517042 | DOI:10.1016/j.tree.2025.05.001

Plant Genome. 2025 Jun;18(2):e70055. doi: 10.1002/tpg2.70055.

ABSTRACT

Leaf rust (LR) and stripe rust (YR), which are caused by Puccinia triticina and Puccinia striiformis, respectively, are among the most devastating wheat rusts worldwide. These diseases can be managed by using genetically resistant cultivars, an economical and environmentally safer alternative to fungicides. Over 100 and 80 Lr and Yr resistance genes have been discovered, respectively; however, rust pathogens are overcoming introduced resistance genes in the southeastern United States. Genome-wide association study has emerged as a valuable tool to identify new LR and YR resistance loci. In this study, a panel of 263 soft red winter wheat genotypes was evaluated for LR and YR severity in Plains, GA, and Williamson, GA, in a randomized complete block design of two replicates during 2019 and 2021-2023. Also, LR and YR infection types were assessed on seedlings at the three leaf stage in three greenhouse trials. A total of 26 significant quantitative trait loci (QTL) explaining 0.6%-30.8% phenotypic variance (PV) was detected by at least two of the five GAPIT models (BLINK, CMLM, FarmCPU, GLM, and MLM) tested. Nine major QTL included QLrYr-2A.1 linked to single-nucleotide polymorphism S2A_20855466, which had the highest overall PV (30.8%) for response to both rust pathogens in the field. Using the Chinese Spring Reference Genome Version 1.0, we detected 16 candidate genes, and four known R genes and QTL overlapped two major QTL. Of these QTL, 16 are likely novel genetic loci with potential for marker-assisted selection.

PMID:40495572 | DOI:10.1002/tpg2.70055

Phytopathology. 2025 Jun 11. doi: 10.1094/PHYTO-04-25-0143-SC. Online ahead of print.

ABSTRACT

Root-knot nematodes (Meloidogyne spp.) are a continuing threat to soybean production, with M. incognita being the predominant species. The deployment of Mi-resistant soybean cultivars is a primary management strategy, but the underlying molecular mechanisms contributing to resistance remain unknown. A single, additive gene for resistance to M. incognita, Rmi1, was previously identified in soybean cv. Forrest and associated with the emigration of second-stage juveniles from the roots. To better understand the Rmi1-mediated resistance response, we used Forrest-derived F₅ RILs differing for Rmi1 to analyze global changes in gene expression in response to M. incognita infection at 2- and 4-days post inoculation. We identified 1,471 differentially expressed (DE) genes in the compatible interaction and 1,037 DE genes in the incompatible interaction. Forty-five percent of DE genes were DE in both interactions, 42% (856) were unique to the compatible interaction, and 13% (261) were unique to the incompatible interaction. Genes uniquely DE in the incompatible interaction included genes involved in cell wall modification, hormone signaling, endomembrane trafficking, and redox reactions providing new insights into the resistance mechanism mediated by Rmi1 in soybean to root-knot nematodes.

PMID:40498525 | DOI:10.1094/PHYTO-04-25-0143-SC

BMC Plant Biol. 2025 Jun 5;25(1):766. doi: 10.1186/s12870-025-06799-x.

ABSTRACT

BACKGROUND: Fruit ripening is a coordinated process that leads to an increase in sugars, decrease in acids and accumulation of pigments. Blueberry fruit exhibit an atypical climacteric ripening behavior. These fruit display an increase in respiration and ethylene production during ripening, however ethylene synthesis is developmentally regulated. In this study, the effect of ethylene on blueberry fruit ripening was investigated via preharvest applications of ethylene-releasing plant growth regulators (PGRs), ethephon and 1-aminocyclopropane 1-carboxylic acid (ACC), in one southern highbush cultivar, Miss Lilly in 2019, and two rabbiteye cultivars, Premier and Powderblue in 2019 and 2020. Further, the effects of these two PGRs on fruit metabolism during ripening in the two rabbiteye cultivars, and postharvest fruit quality in all three cultivars were evaluated.

RESULTS: Both PGRs increased ethylene evolution within 1-3 days after treatment (DAT). Ethephon and ACC applications increased the rate of ripening within 5 DAT in all cultivars, and increased ripe (blue) fruit by up to 35% and 29%, respectively between 7 to 10 DAT compared to the control. Metabolite analysis revealed that PGR treatments resulted in an immediate, but transient increase in sucrose, glucose and fructose, in ‘Premier’ at 3 DAT. Malate decreased at 3 DAT in response to both PGR treatments in ‘Premier’, and at 5 DAT in ethephon treatment in both cultivars. A rapid increase in the concentration of multiple anthocyanins was noted at 3 DAT in response to both PGRs in ‘Premier’ and ‘Powderblue’. Gene expression analysis revealed an increase in transcript abundance of VACUOLAR INVERTASE (vINV) and multiple anthocyanin biosynthesis genes between 1 and 3 DAT after PGR treatments in both cultivars, supporting the metabolite changes. However, the alteration in fruit metabolite concentrations were not sustained, and similar in PGR-treated fruit compared to the control in ripe fruit harvested at 10 DAT. Postharvest fruit quality attributes, such as firmness, total soluble solids, titratable acidity, and visual quality, were not consistently affected by the PGR applications compared to control treatments across all cultivars. A decrease in fruit weight was noted, although not consistently, in response to PGR treatments.

CONCLUSIONS: Overall, this study demonstrates that ethylene plays a crucial role in promoting ripening via rapid and transient stimulation of sugar, acid and anthocyanin metabolism. The promotion of fruit ripening by ethylene-releasing PGRs can lead to minimal but inconsistent changes in fruit quality attributes during postharvest storage.

PMID:40474063 | DOI:10.1186/s12870-025-06799-x

Plant Commun. 2025 Jun 3:101393. doi: 10.1016/j.xplc.2025.101393. Online ahead of print.

ABSTRACT

Teucrium chamaedrys, also called wall germander, is a small woody shrub native to the Mediterranean region. Its name is derived from the Greek words meaning ‘ground oak’, since its tiny leaves resemble those of an oak tree. Teucrium species are proliferative producers of diterpenes, which afford them valuable properties widely co-opted in traditional and western medicines. Sequence and assembly of the 3 Gbp tetraploid T. chamaedrys revealed 74 diterpene synthase genes, with the vast representation of these diterpene synthases clustered along four genomic loci. Comparative genomics revealed that this cluster is mirrored in the closely related species, Teucrium marum. Along with the presence of several cytochrome p450 sequences, this region is the one of largest biosynthetic gene clusters identified. Teucrium is well known for accumulating clerodane-type diterpenoids which are produced from a kolavanyl diphosphate precursor. To elucidate the complex biosynthetic pathways of these medicinal compounds, we identified and functionally characterized several kolavanyl diphosphate synthases from T. chamaedrys. Its remarkable chemistry and tetraploidy make T. chamaedrys an interesting and unique model for studying genomic evolution and adaptation in plants.

PMID:40468595 | DOI:10.1016/j.xplc.2025.101393

Annu Rev Phytopathol. 2025 Jun 4. doi: 10.1146/annurev-phyto-121823-080201. Online ahead of print.

ABSTRACT

Necrotrophic bacteria within the order Enterobacterales cause significant agricultural losses, with few effective management options available for producers. These pathogens have evolved at least two distinct strategies for infecting plants. Soft rot pathogens in the family Pectobacteriaceae, such as Dickeya and Pectobacterium, rely on secreting plant cell wall-degrading enzymes. In contrast, Pantoea necrotrophs depend on the production of phosphonate phytotoxins, a type of secondary metabolite, for their pathogenicity. This review summarizes recent discoveries on the virulence mechanisms of bacterial necrotrophs and current knowledge of factors that influence their host range and interactions with plant immune defenses. A deeper understanding of bacterial necrotroph host range determinants could inform the development and deployment of enhanced genetic resistance strategies.

PMID:40465659 | DOI:10.1146/annurev-phyto-121823-080201

PLoS Genet. 2025 Jun 2;21(6):e1011735. doi: 10.1371/journal.pgen.1011735. Online ahead of print.

ABSTRACT

In ciliates, cortical organelles, including ciliary arrays, are positioned at precise locations along two polarity axes: anterior-posterior and circumferential (lateral). We explored the poorly understood mechanism of circumferential patterning, which generates left-right asymmetry. The model ciliate Tetrahymena has a single anteriorly-located oral apparatus. During cell division, a single new oral apparatus forms near the equator of the parental cell and along the longitude of the parental organelle. Cells homozygous for hypoangular 1 (hpo1) alleles, assemble multiple oral apparatuses positioned either to the left or right flanking the normal oral longitude. Using comparative next-generation sequencing, we identified HPO1 as a gene encoding an ARMC9-like protein. Hpo1 colocalizes with the ciliary basal bodies, forming a bilateral concentration gradient, with the high point on the cell’s right side and a sharp drop-off that marks the longitude at which oral development initiates on the ventral side. A second Hpo1 concentration drop-off is present on the dorsal surface, where it marks the position for development of a cryptic oral apparatus that forms in the janus mutants. Hpo1 acts bilaterally to exclude oral development from the cell’s right side. Hpo1 interacts with the Beige-Beach domain protein Bcd1, a cell’s left side-enriched factor, whose loss also confers multiple oral apparatuses on the ventral surface. A loss of both Hpo1 and Bcd1 is lethal and profoundly disrupts the positioning, organization and size of the forming oral apparatus (including its internal left-right polarity). We conclude that in ciliates, the circumferential patterning involves gradient-forming factors that are concentrated on either the cell’s right or left side and that the two sides of the cortex interact to create boundary effects that induce, position and shape developing cortical organelles.

PMID:40455876 | DOI:10.1371/journal.pgen.1011735

Plant Dis. 2025 May 22. doi: 10.1094/PDIS-01-25-0117-SR. Online ahead of print.

ABSTRACT

Alternaria brassicicola is the causal agent typically associated with Alternaria leaf blight and head rot (ABHR) disease in broccoli and related crops in the Eastern United States. Recently a new species, A. japonica, has been reported as causing disease in broccoli and other vegetables in this region. We conducted a multi-state pathogen survey during the growing seasons of 2022 and 2023 to assess the distribution and occurrence of A. japonica in relation to A. brassicicola in five broccoli-producing states. Our approach specifically targeted collection of broccoli leaves with lesions typical of ABHR within commercially grown fields managed using either organic or conventional approaches in Connecticut, Massachusetts, New York, Virginia, and Georgia. Only typical ABHR leaf lesions were selected for pathogen isolation and, subsequently, sequencing of the Alternaria major allergen a1 gene was used to identify Alternaria species. The predominant species isolated was A. brassicicola (88% in 2022 and 94% in 2023) and the second most common was A. alternata (12% in 2022 and 6% in 2023), which was obtained from fields in Connecticut and Massachusetts in 2022, and in Virginia in both years. Alternaria japonica was not found in either year. Symptoms of A. alternata were indistinguishable from A. brassicicola, as were colony morphologies. While A. alternata is considered a generalist and of little consequence for broccoli, it is considered a pathogen of significance on multiple crops (blueberry, citrus, pistachios), but there remains scant information on the disease etiology on broccoli. Therefore, we inoculated broccoli with A. alternata in controlled conditions in order to shed light on possible differences in infectivity of these species on broccoli. Results of our study showed that A. alternata is pathogenic on broccoli, capable of initiating infection and causing lesions typical of ABHR. This indicates that future disease surveys of ABHR should conclusively identify species of Alternaria that are causing disease. Additional research is needed to determine the significance of this finding in relation to yield impacts, epidemiology, fungicide resistance, and management recommendations.

PMID:40403277 | DOI:10.1094/PDIS-01-25-0117-SR

Sci Adv. 2025 May 23;11(21):eadw3433. doi: 10.1126/sciadv.adw3433. Epub 2025 May 21.

ABSTRACT

Activation of synthetic centromeres on chromosome 4 in maize leads to its breakage and formation of trisomic fragments called neochromosomes. A limitation of neochromosomes is their low and unpredictable transmission rates due to trisomy. Here, we report that selecting for dicentric recombinants through male crosses uncovers stabilized chromosome 4 fission events, which split it into 4a-4b complementary chromosome pairs, where 4a carries a native centromere and 4b carries a synthetic one. The cells rapidly stabilized chromosome ends by de novo telomere formation, and the new centromeres spread among genes without altering their expression. When both 4a and 4b chromosomes were made homozygous, they segregated through meiosis indistinguishably from wild type and gave rise to healthy plants with normal seed set, indicating that the synthetic centromere was fully functional. This work leverages synthetic centromeres to engineer chromosome fission, raising the diploid chromosome number of maize from 20 to 22.

PMID:40397737 | PMC:PMC12094224 | DOI:10.1126/sciadv.adw3433

Plant Methods. 2025 May 20;21(1):66. doi: 10.1186/s13007-025-01375-8.

ABSTRACT

High resolution three-dimensional (3D) point clouds enable the mapping of cotton boll spatial distribution, aiding breeders in better understanding the correlation between boll positions on branches and overall yield and fiber quality. This study developed a segmentation workflow for point clouds of 18 cotton genotypes to map the spatial distribution of bolls on the plants. The data processing workflow includes two independent approaches to map the vertical and horizontal distribution of cotton bolls. The vertical distribution was mapped by segmenting bolls using PointNet++ and identifying individual instances through Euclidean clustering. For horizontal distribution, TreeQSM segmented the plant into the main stem and individual branches. PointNet++ and Euclidean clustering were then used to achieve cotton boll instance segmentation. The horizontal distribution was determined by calculating the Euclidean distance of each cotton boll relative to the main stem. Additionally, branch types were classified using point cloud meshing completion and the Dijkstra shortest path algorithm. The results highlight that the accuracy and mean intersection over union (mIoU) of the 2-class segmentation based on PointNet++ reached 0.954 and 0.896 on the whole plant dataset, and 0.968 and 0.897 on the branch dataset, respectively. The coefficient of determination (R²) for the boll counting was 0.99 with a root mean squared error (RMSE) of 5.4. For the first time, this study accomplished high-granularity spatial mapping of cotton bolls and branches, but directly predicting fiber quality from 3D point clouds remains a challenge. This method provides a promising tool for 3D cotton plant mapping of different genotypes, which potentially could accelerate plant physiological studies and breeding programs.

PMID:40394606 | DOI:10.1186/s13007-025-01375-8

Mol Plant Pathol. 2025 May;26(5):e70096. doi: 10.1111/mpp.70096.

ABSTRACT

Harpins are proteins secreted by many gram-negative, plant-pathogenic bacteria that stimulate the hypersensitive reaction (HR), a host cell death defence response, when infiltrated into plant leaves as purified proteins. This activity of harpins was first discovered in Nicotiana tabacum (tobacco), which manifests an especially strong and rapid harpin-activated HR that becomes evident within 12-24 h after infiltration. HrpN is the major harpin of the fire blight pathogen Erwinia amylovora. We discovered natural variation in the HrpN-induced HR among tobacco accessions and identified candidate genes using genetic mapping and bulked-segregant analysis with whole genome sequencing. Virus-induced gene silencing of candidate gene Wall-Associated Kinase 2 (WAK2) abrogated the HR in response to HrpN and HpaG, a harpin from the soybean bacterial pustule pathogen Xanthomonas citri pv. glycines. WAK2 silencing also compromised the avirulence activity of harpin HrpZ in the tobacco wildfire pathogen Pseudomonas syringae pv. tabaci. A natural, disruptive mutation in WAK2 correlated with the inability of tobacco accessions to mount the harpin-mediated HR. We conclude that the predicted receptor-like kinase WAK2 is required for the strong HR induced in tobacco leaves by harpin protein infiltration and can potentially mediate resistance to bacterial pathogens based on harpin recognition.

PMID:40391583 | DOI:10.1111/mpp.70096

mBio. 2025 May 20:e0365224. doi: 10.1128/mbio.03652-24. Online ahead of print.

ABSTRACT

Invasive aspergillosis, caused by Aspergillus fumigatus, represents a critical public health concern, particularly due to increasing resistance to triazole antifungals linked to TR₃₄/TR₄₆ cyp51A haplotypes. In our genomic epidemiology study of 157 A. fumigatus isolates from Dutch environmental hotspots and two clinical centers, we identified near-identical genomes in several environmental and patient isolates, indicating a probable link. However, the geographic and temporal data alone are not sufficient to explain direct transmission pathways. Furthermore, a comparison with more than 1,200 globally sourced genomes revealed the extensive dissemination of certain clonal groups across multiple distant regions, raising significant challenges for the utility of genomic epidemiology. The discovery of high genetic diversity and the widespread distribution of some clonal groups challenges current understanding, suggesting that in most cases, tracing the precise source of individual infections will remain extremely difficult, even with increased sampling. In addition, we uncovered that the multi-triazole-resistant TR₃₄/TR₄₆ cyp51A haplotypes are associated with resistance to non-triazole fungicides such as benzimidazole, succinate dehydrogenase inhibitor, and quinone outside inhibitor classes, strongly suggesting an exposure history to multiple agricultural fungicides in these environmental hotspots. This resistance beyond the azole class suggests that strategies targeting only triazoles may be insufficient. Our findings challenge current paradigms and carry significant implications for One Health research and global public health strategies, underscoring the urgency of multidisciplinary approaches to tracking and monitoring fungal resistance.IMPORTANCEOur study links triazole-resistant A. fumigatus isolates cultured from three environmental hotspots to cases of aspergillus disease in two hospitals in the Netherlands. Genome comparisons of isolates from environmental hotspots and patients showed multiple near-identical linked genotypes, consistent with a route of transmission from the environment to patients. Linked cases without clear transmission routes emphasize the need to better understand the ecology of this fungus. Since patients often do not visit rural hotspots, research should explore complex, long-distance transmission mechanisms, including airborne dispersal of conidia or non-agricultural habitats. The multi-fungicide resistance phenotype suggests reducing one class of fungicides alone may not lower resistance selection. Instead, interventions should target modifying environments that promote the growth of fungicide-resistant A. fumigatus and prevent the escape of resistant spores from these hotspots to mitigate the burden of environmental resistance effectively.

PMID:40391955 | DOI:10.1128/mbio.03652-24

Integr Comp Biol. 2025 May 8:icaf028. doi: 10.1093/icb/icaf028. Online ahead of print.

ABSTRACT

Climate change is simultaneously increasing atmospheric carbon dioxide concentrations ([CO2]) and temperatures. We conducted a multi-factorial growth chamber experiment to examine how these climate change factors interact to influence the expression of ecologically-relevant traits, clines in these traits, and natural selection on morphology and phenology of diverse accessions of Boechera stricta (Brassicaceae) sourced from a broad elevational gradient in Colorado, USA. Plastic shifts in a key allocation trait (root mass fraction) in response to temperature accord with the direction of selection for probability of flowering, indicating that plasticity in this trait could be adaptive. However, plasticity in a foliar functional trait (leaf dry matter content) in response to temperature and [CO2] did not align with the direction of selection, indicating that plasticity could reduce fitness based on plant carbon allocation strategies. For another ecologically-important phenotype, selection favors resource acquisitive trait values (higher specific leaf area) under elevated [CO2] and resource conservative trait values (lower specific leaf area) at lower [CO2], despite the lack of plasticity in this trait. This pattern of selection counters published reports that elevated [CO2] induces low specific leaf area but could enable plants to reproduce across a greater period of the growing season under increasingly warm climates. Indeed, warmer temperatures prolonged the duration of flowering. This plasticity is likely adaptive, as selection favored increased flowering duration in the higher temperature treatment level. Thus, the two major results that emerged from our study are that climate change could impose novel and unanticipated patterns of natural selection on plant traits and that plasticity in these traits can be a maladaptive response to stress.

PMID:40338630 | DOI:10.1093/icb/icaf028

Ecol Lett. 2025 May;28(5):e70134. doi: 10.1111/ele.70134.

ABSTRACT

Species’ distributions are changing around the planet as a result of global climate change. Most research has focused on shifts in mean climate conditions, leaving the effects of increased environmental variability comparatively underexplored. This paper proposes two new macroecological hypotheses-the variability damping hypothesis and the variability adaptation hypothesis-to understand how ecological dynamics and evolutionary history could influence biogeographic patterns being forced by contemporary large-scale climate change across all major ecosystems. The variability damping hypothesis predicts that distributions of species living in deep water environments will be least affected by increasing climate-driven temperature variability compared with species in nearshore, intertidal and terrestrial environments. The variability adaptation hypothesis predicts the opposite. Where available, we discuss how the existing evidence aligns with these hypotheses and propose ways in which they may be empirically tested.

PMID:40344332 | PMC:PMC12061546 | DOI:10.1111/ele.70134

Int J Mol Sci. 2025 Apr 23;26(9):3999. doi: 10.3390/ijms26093999.

ABSTRACT

The mechanisms underlying leaf variegation in the ornamental Ilex × ‘Solar Flare’ remain poorly understood. To investigate this phenomenon, we conducted a comprehensive characterization of its variegated leaves. Compared to green sectors, yellow sectors exhibited severe chloroplast structural abnormalities, including swollen chloroplasts, damaged thylakoid membranes, and reduced chloroplast numbers. These yellow sectors also showed significantly lower chlorophyll and carotenoid levels, along with a depletion of key chlorophyll precursors-protoporphyrin IX (Proto IX), magnesium protoporphyrin IX (Mg-Proto IX), and protochlorophyllide (Pchlide). Photosynthetic efficiency was significantly impaired. Comparative transcriptome analysis identified 3510 differentially expressed genes (DEGs) between yellow and green sectors. Key disruptions in chlorophyll biosynthesis included upregulated CHLD expression and downregulated CHLH and CHLG expression, leading to impaired chlorophyll synthesis. Additionally, chlorophyll degradation was accelerated by PAO upregulation. Defective chloroplast development in yellow sectors was associated with the downregulation of GLK1, GLK2, and thylakoid membrane-related genes (PsbC, PsbO, PsbR, PsaD, and PsaH). These molecular alterations likely drive the variegated phenotype of I. × ‘Solar Flare’. These observations advance our understanding of the genetic and physiological mechanisms regulating leaf variegation in this cultivar.

PMID:40362242 | PMC:PMC12071917 | DOI:10.3390/ijms26093999

Molecules. 2025 Apr 30;30(9):2020. doi: 10.3390/molecules30092020.

ABSTRACT

The discovery of bioactive natural products is often challenged by the complexity of isolating and characterizing active compounds within diverse mixtures. Previously, we introduced a ¹H NMR-based weighted gene correlation network analysis (WGCNA) approach to identify spectral features linked to growth inhibitory activity of Piper (Piperaceae) leaf extracts against model plant, fungal, and bacterial organisms. This method enabled us to prioritize specific spectral features linked to bioactivity, offering a targeted approach to natural product discovery. In this study, we validate the predictive capacity of the WGCNA by isolating the compounds responsible for the bioactivity-associated resonances and confirming their antifungal efficacy. Using growth inhibition assays, we verified that the isolated compounds, including three novel antifungal agents, exhibited significant bioactivity. Notably, one of these compounds contains a rare imidazolium heterocyclic motif, marking a new structural class in Piper. These findings substantiate the ¹H NMR-based WGCNA as a reliable tool for identifying structural types associated with biological activity, streamlining the process of discovering bioactive natural products in complex extracts.

PMID:40363825 | PMC:PMC12073215 | DOI:10.3390/molecules30092020

Genetics. 2025 May 14:iyaf091. doi: 10.1093/genetics/iyaf091. Online ahead of print.

ABSTRACT

In maize, there are two meiotic drive systems that target large heterochromatic knobs composed of tandem repeats known as knob180 and TR-1. The first meiotic drive haplotype, Abnormal chromosome 10 (Ab10) confers strong meiotic drive (∼75% transmission as a heterozygote) and encodes two kinesins: KINDR, which associates with knob180 repeats and TRKIN, which associates with TR-1 repeats. Prior data show that meiotic drive is conferred primarily by the KINDR/knob180 system while the TRKIN/TR-1 system seems to have little or no role, making it unclear why Trkin has been maintained in Ab10 haplotypes. The second meiotic drive haplotype, K10L2, confers a low level of meiotic drive (∼51-52%) and only encodes the TRKIN/TR-1 system. Here we used long-read sequencing to assemble the K10L2 haplotype and showed that it has strong homology to an internal portion of the Ab10 haplotype. We also carried out CRISPR mutagenesis to test the role of Trkin on Ab10 and K10L2. The data indicate that the Trkin gene on Ab10 does not improve drive or fitness but instead has a weak deleterious effect when paired with a normal chromosome 10. The deleterious effect is more severe when Ab10 is paired with K10L2: in this context functional Trkin on either chromosome nearly abolishes Ab10 drive. Mathematical modeling based on the empirical data suggest that Trkin is unlikely to persist on Ab10. We conclude that Trkin either confers an advantage to Ab10 in untested circumstances or that it is in the process of being purged from the Ab10 population.

PMID:40365704 | DOI:10.1093/genetics/iyaf091