Category: Pub Med

Nucleic Acids Res. 2025 Nov 26:gkaf1287. doi: 10.1093/nar/gkaf1287. Online ahead of print.

ABSTRACT

Polyploidy and small-scale duplication have repeatedly reshaped plant genomes, making synteny and colinearity indispensable for evolutionary inference. We present PGDD 2.0 (accessible at chibba.agtec.uga.edu and pgdd2.org), a major update to the Plant Genome Duplication Database (PGDD) that now aggregates >120 complete telomere-to-telomere (T2T) assemblies, including many chromosome-scale genomes spanning all major Viridiplantae lineages. Each genome sequence is processed with a standardized pipeline to call intra- and intergenomic colinear (syntenic) blocks, estimate Ks, and block score metrics and age distributions. PGDD 2.0 introduces (i) interactive synteny networks for pattern discovery across taxa, (ii) a “riparian” or synteny alignment view for visualizing mesosynteny and rearrangements, and (iii) an embedded SynVisio module for rendering user-supplied or PGDD-downloaded MCScanX results directly in the browser. Together, these advances support tasks from resolving ancient whole-genome duplication signatures to tracing the postduplication fates of specific gene families with T2T-level precision and beyond. PGDD 2.0 delivers an up-to-date, uniform, and user-centered platform for plant comparative genomics, accelerating discovery regarding polyploidy, gene duplication, and genome evolution.

PMID:41296551 | DOI:10.1093/nar/gkaf1287

Physiol Plant. 2025 Nov-Dec;177(6):e70655. doi: 10.1111/ppl.70655.

ABSTRACT

The use of microorganisms is a promising technique in agriculture to provide greater water and nutrient efficiency for crops. The objective of this study was to evaluate the effects of microbial inoculation on plant growth, fruit yield and fruit quality of cherry tomatoes (Solanum lycopersicum var. cerasiforme) in a protected environment. The experiment was arranged in a randomized block design with three treatments: (i) inoculation with Bacillus subtilis ATCC 23858; (ii) inoculation with Burkholderia seminalis TC3.4.2R3; and (iii) non-inoculation, with eight replications. The data were subjected to ANOVA using the F-test followed by the Tukey test (p < 0.05) and multivariate statistical analysis for principal component analysis. B. seminalis led to a higher germination rate, increased fruit yield (FY) by 4.3% and soluble solids content (SSC) of 12.33% compared to the non-inoculation treatment. B. subtilis increased plant height (PH) and root mass, FY by 9.56% and SSC by 9.25%. Inoculation increased the mechanical resistance of fruits in terms of compression and puncture. The results of this work indicated that the initial growth of cherry tomatoes was increased by inoculation with B. subtilis and B. seminalis, bringing new possibilities for the sustainable production of this crop since inoculation promoted plant growth, increased FY and improved fruit quality. The study suggests that inoculation with specific strains of B. subtilis and B. seminalis can be beneficial for cherry tomato cultivation in protected environments, highlighting the use of microorganisms in agriculture and their potential for sustainable and efficient crop management.

PMID:41292417 | DOI:10.1111/ppl.70655

Appl Environ Microbiol. 2025 Nov 25:e0164325. doi: 10.1128/aem.01643-25. Online ahead of print.

ABSTRACT

Pseudomonas alliivorans is an important emerging pathogen affecting numerous crops. The species is closely related to Pseudomonas viridiflava, with which P. alliivorans strains were often misidentified in the past. Here, we investigated the genetic and pathogenic characteristics of P. alliivorans strains isolated primarily from onions and weeds in Georgia, USA, using whole-genome sequencing, comparative genomics, and functional assays. We delineated the core genome and genetic diversity of these isolates, assessed their pathogenicity on onion foliage and red onion scales, and examined the roles of key virulence determinants (Hrp1-type III secretion system [T3SS], rhizobium-T3SS, type II secretion systems [T2SSs], and thiosulfinate [allicin]-tolerance alt cluster). Our results showed that the Hrp1-T3SS is pivotal for pathogenicity in P. alliivorans, whereas the rhizobium-T3SS, T2SSs, and alt cluster do not contribute to symptom development on red onion scales. Notably, the alt cluster confers in vitro thiosulfinate tolerance, supporting bacterial survival against onion-derived antimicrobial compounds. Additionally, homologous recombination in P. alliivorans occurs infrequently (at approximately one-tenth the rate of point mutations) and involves divergent DNA segments. The alt cluster is acquired through horizontal gene transfer, as evidenced by its lower GC content and the presence of adjacent transposases. In summary, our research provides valuable insights into the genetic diversity, evolutionary dynamics, and virulence mechanisms of P. alliivorans strains from Georgia, USA.IMPORTANCEPseudomonas alliivorans is an emerging plant pathogen that threatens onion and other plants of economic importance. This study identifies key traits that help this bacterium cause disease, such as a specific secretion system critical for infecting onions, and a gene cluster that aids bacterial survival in onion tissues. Beyond highlighting weed as a potential inoculum source and supporting better weed management, the findings of this research open avenues for more targeted disease menegement. By unraveling the genetics of this pathogen, we can develop improved ways to detect, prevent, and reduce its impact, protecting crop health and yields.

PMID:41288358 | DOI:10.1128/aem.01643-25

Proc Natl Acad Sci U S A. 2025 Dec 2;122(48):e2514628122. doi: 10.1073/pnas.2514628122. Epub 2025 Nov 24.

ABSTRACT

CO₂ fertilization of the terrestrial biosphere is limited by nitrogen. Biological nitrogen fixation (BNF) is the dominant natural nitrogen source to the terrestrial biosphere and can alleviate nitrogen limitation but is poorly constrained in Earth system models (ESMs). Here, we compare terrestrial BNF from an ensemble of ESMs of the 6th Coupled Model Intercomparison Project to a new global synthesis of observations across natural and agricultural biomes. We find that compared to observations, ESMs underestimate agricultural BNF but overestimate natural BNF in the present day by over 50%. Natural BNF is overestimated in the most productive ecosystems that contribute most to the terrestrial carbon sink (forests and grasslands). ESMs with different BNF representations yield a range of BNF responses to CO₂ enrichment. Some ESMs with phenomenological representations of BNF predict a natural BNF increase in response to a doubling of CO₂ that aligns with a meta-analysis of CO₂ enrichment experiments (31% increase) but fail to account for the substantial carbon cost of BNF. In contrast, ESMs with mechanistic representations of BNF account for its carbon cost as well as its regulation by nitrogen limitation but overestimate the BNF response to a doubling of CO₂ (135% increase). Overall, all current BNF representations in ESMs fall short of fully capturing its response to rising atmospheric CO₂. Finally, we find a positive correlation between modeled present-day natural BNF and the CO₂ fertilization effect across ESMs, suggesting that overestimated natural BNF translates to an exaggerated CO₂ fertilization effect of approximately 11% in ESMs.

PMID:41284886 | DOI:10.1073/pnas.2514628122

Cell Rep. 2025 Nov 22;44(12):116603. doi: 10.1016/j.celrep.2025.116603. Online ahead of print.

ABSTRACT

In the human fungal pathogen Cryptococcus deneoformans, sexual reproduction facilitates evolution and adaptation. This fungus can undergo two sexual modes: α × a sexual reproduction and unisexual reproduction (without mating partner cooperation), with α-unisexual reproduction predominating. However, the mechanism driving commitment to α-unisexual reproduction has remained elusive. Here, through a multilayered genetic screen of transfer DNA (T-DNA) insertional mutants, we identified several mutants with enhanced unisexual reproduction but impaired α × a heterothallic mating. Genome sequencing of these mutants revealed that the T-DNA insertions are enriched in genes involved in respiration. Consistently, pharmacological inhibition of respiration recapitulated this phenotype. This respiratory-inhibition-prompted selection for unisexual development requires the filamentation activator Znf2, which directly inhibits the cyclin Cln1, resulting in cell-cycle arrest in the G2/M phase, which promotes unisexual development but functionally excludes α × a heterothallic mating. Collectively, our findings uncover a mechanism that commits unisexual reproduction through respiratory inhibition.

PMID:41275490 | DOI:10.1016/j.celrep.2025.116603

Science. 2025 Nov 20;390(6775):786-787. doi: 10.1126/science.aec7902. Epub 2025 Nov 20.

ABSTRACT

Chromosome engineering produces a reduced eight-chromosome karyotype in Arabidopsis thaliana.

PMID:41264719 | DOI:10.1126/science.aec7902

J Econ Entomol. 2025 Nov 19:toaf321. doi: 10.1093/jee/toaf321. Online ahead of print.

ABSTRACT

Host plant resistance (HPR) has shown potential for suppressing sweetpotato whitefly, Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae), in smooth (glabrous) crop varieties lacking leaf trichomes. The objective of this study was to investigate the interaction between HPR and insecticidal control, aiming to enhance their collective efficacy in whitefly management. Field trials were conducted in cotton and cantaloupe planted as strip crops at 2 locations in southern Georgia, United States: Tifton and Camilla. Treatments comprised 2 insecticides, based on the active ingredients pyriproxyfen and cyantraniliprole, with 2 different trichome conditions: pubescent (hairy), or smooth varieties. During the crop growing season, B. tabaci adult, egg, and nymph populations were monitored, and whitefly preferences were evaluated. Results indicate a preference of whiteflies for cotton and cantaloupe pubescent varieties, largely attributed to the presence of leaf trichomes. Pyriproxyfen predominantly reduced nymph populations, while cyantraniliprole was effective against both immatures and adults. Significant interactions among crop type, trichome presence, and insecticide application in determining B. tabaci abundance were measured. The glabrous cotton variety demonstrated greater whitefly suppression compared to glabrous melon, and cyantraniliprole exhibited a heightened initial mortality in pubescent cultivars. The study underscores the importance of selecting smooth leaf crop varieties in integrated B. tabaci management strategies. The results illuminate the need for developing real-world testing models with compatible strategies of integrated pest management (IPM) programs for B. tabaci and provide a wide-ranging insight into the interactive effects and dependency of multiple components involved in whitefly control in multicropping systems.

PMID:41259812 | DOI:10.1093/jee/toaf321

ACS Synth Biol. 2025 Nov 18. doi: 10.1021/acssynbio.5c00614. Online ahead of print.

ABSTRACT

Iron is a critical micronutrient for both plants and humans, yet its declining availability across agricultural systems threatens global food security and health. Biofortification of food crops has emerged as a promising strategy to combat iron deficiency and anemia, leveraging both crop breeding and microbiome-based approaches to enhance iron mobilization and uptake. Advances in plant and bacterial synthetic biology could enable the precise programming of iron homeostasis and acquisition mechanisms, offering tailored solutions across diverse species and environments. Here, we outline key biomolecules, genes, and biosynthetic and transport pathways that represent underexplored synthetic biology targets for improving crop iron acquisition. We highlight opportunities to tune expression strength, tissue specificity, and cross-host pathway transfer to enhance chelation- and reduction-mediated solubilization of soil iron and augment plant uptake. Finally, we emphasize the broader importance of developing plant-microbe-metal actuators as modular components in genetic circuit design and discuss how their deployment across diverse plant and microbial chassis could accelerate agricultural biofortification and improve global nutrition.

PMID:41252749 | DOI:10.1021/acssynbio.5c00614

Plant J. 2025 Nov;124(4):e70554. doi: 10.1111/tpj.70554.

ABSTRACT

Climate uncertainty is intensifying the need for greater plasticity in carbohydrate reserve utilization to support winter survival and spring growth in woody perennials. In poplar, the single-copy SUT4, which encodes a tonoplast-localized sucrose transporter, and the SUT5/SUT6 genome duplicates, which encode plasma membrane-localized transporters, are expressed year-round, with SUT4 showing the highest expression during cool seasons. Given its role in vacuolar sucrose efflux and winter-predominant expression, SUT4 may play a key role in modulating seasonal carbohydrate dynamics. While SUT4-knockdown and knockout effects have been studied under greenhouse conditions, their impact under field conditions remains unexplored. Here, we report a field-based study comparing CRISPR knockout mutants of winter-expressed SUT4 and SUT5/SUT6 in Populus tremula × alba. We show that sut4, but not sut5/6, mutants exhibited earlier autumn leaf senescence, delayed spring bud flush, reduced stem growth, and altered sugar partitioning in winter xylem and bark relative to controls. After 2 years in the field, all genotypes flowered before leaf flush in early spring; however, sut4 mutants produced sterile ovules despite developing normal-looking catkins. Metabolic profiling revealed disrupted sucrose and raffinose dynamics in elongating sut4 catkins. This was accompanied by transcriptomic signatures of elevated stress and downregulation of proanthocyanidin biosynthesis and circadian clock genes. These findings highlight the critical role of SUT4 in coordinating sugar allocation, stress responses, and seasonal development in poplar.

PMID:41241958 | DOI:10.1111/tpj.70554

Plants (Basel). 2025 Oct 31;14(21):3337. doi: 10.3390/plants14213337.

ABSTRACT

Climate change is shifting where suitable habitats occur for many species across the planet. Sarracenia purpurea L., the most widely distributed pitcher plant species in North America, already faces significant threats from land use change. While S. purpurea is well studied at physiological and local scales, threat assessments for this species at biogeographic scales are absent. Here, we remedy this by using Habitat Suitability Models to predict current suitable habitats and estimate climate-based shifts in the suitable habitat for S. purpurea in the near (2040) and long term (2100). The models predicted large areas of habitat loss in the southeastern United States and the western portion of the Great Lakes region by 2040. While the models also predict significant gains in suitable habitats north of the current S. purpurea range, the limited dispersal ability of this species precludes the possibility of natural migration to newly suitable habitats. Our results suggest that the degradation of considerable portions of current suitable habitats is already occurring and will continue in the future. Particularly threatened are the southern subspecies (e.g., Sarracenia purpurea subsp. venosa) of S. purpurea. We therefore urge land managers to make conservation efforts targeting threatened subspecies and encourage further the biogeographic investigation of less widely distributed congenerics of S. purpurea.

PMID:41225887 | PMC:PMC12608460 | DOI:10.3390/plants14213337