Category: Pub Med

New Phytol. 2025 Nov 2. doi: 10.1111/nph.70700. Online ahead of print.

ABSTRACT

Myrothamnus flabellifolia is a dioecious resurrection plant endemic to southern Africa that has become an important model for understanding desiccation tolerance. Despite its ecological and medicinal significance, genomic and transcriptomic resources for the species are limited. We generated a chromosome-level, haplotype-resolved reference genome assembly and annotation for M. flabellifolia and conducted transcriptomic profiling across a natural dehydration-rehydration time course in the field. Genome architecture and sex determination were characterized, and co-expression network and cis-regulatory element (CRE) enrichment analyses were used to investigate dynamic responses to desiccation. The 1.28-Gb genome exhibits unusually consistent chromatin architecture with unique chromosome organization across highly divergent haplotypes. We identified an XY sexual system with a small sex-determining region on Chromosome 8. Transcriptomic responses varied with dehydration severity, pointing to early suppression of growth, progressive activation of protective mechanisms, and subsequent return to homeostasis upon rehydration. Late embryogenesis abundant and early light-induced protein transcripts were dynamically regulated and showed enrichment of abscisic acid and stress-responsive CREs pointing toward conserved responses. Together, this study provides foundational resources for understanding the genomic architecture and reproductive biology of M. flabellifolia and offers new insights into the mechanisms of desiccation tolerance.

PMID:41178124 | DOI:10.1111/nph.70700

Methods Mol Biol. 2026;2987:231-252. doi: 10.1007/978-1-0716-5001-1_16.

ABSTRACT

Reproduction of apomictic and sexual plants within Cenchrus, previously classified as both Cenchrus and Pennisetum, has been studied since the 1950s. Seventeen of approximately 108-120 Cenchrus species contain apomictic cytotypes. Apomictic cytotypes are polyploids and all are classified as developing via apospory. While most apomictic species in Cenchrus produce viable offspring that are highly maternally clonal, the ability for sexual reproduction has been retained. With advancement in molecular technologies, understanding the genetic composition, physical location, and genes associated with apospory has been forthcoming. Additional gains including whole-genome assembly of Cenchrus species to study the evolutionary mechanisms underlying apomixis are on the horizon.

PMID:41165987 | DOI:10.1007/978-1-0716-5001-1_16

Theor Appl Genet. 2025 Oct 29;138(11):286. doi: 10.1007/s00122-025-05065-w.

ABSTRACT

The RKN resistance locus Rmi1 was fine-mapped to two genes on chromosome 10, a glycosyl hydrolase family 9 β-1,4-endoglucanase gene and a type I pectin methylesterase gene. Root-knot nematodes (Meloidogyne spp.) are a serious threat to soybean production in the southeast USA, with yield losses of more than $165 million in 2023. Development and deployment of resistant soybean cultivars is the most effective strategy for managing these nematode pests; however, the identity of the resistance genes and underlying mechanism of resistance remains obscure. An additive resistance gene, Resistance to M. incognita-1 (Rmi1), to the predominant species, was first identified in soybean cultivar Forrest but never mapped to a genomic region. Multiple mapping studies have identified a major quantitative trait locus (QTL) with additive action on chromosome 10. In this study, a population consisting of 170 F_2:3 families derived from a cross of Bossier (susceptible) × Forrest (resistant) was initially used to confirm that Rmi1 is in the chromosome 10 QTL. Subsequently, 884 F_5:6 recombinant inbred lines (RILs) derived from the same cross were used to fine-map the Rmi1 causal gene(s) to two genes – a β-1,4-endoglucanase (Glyma.10G017000, EG) and a pectin methylesterase/methylesterase inhibitor (Glyma.10G017100, PME1). Both gene candidates have the potential to play a role in the resistance response to M. incognita. Both gene promoters harbor SNPs and indels and the encoded proteins exhibit amino acid polymorphisms, including a premature stop in PME1 of resistant soybeans. Additionally, both genes show a higher expression level in susceptible roots compared to resistant roots in the absence of infection. This suggests that Rmi1 may confer one or more pre-existing differences related to cell wall modification in soybean roots, ultimately leading to a decrease in susceptibility.

PMID:41160124 | DOI:10.1007/s00122-025-05065-w

Biotechnol Biofuels Bioprod. 2025 Oct 27;18(1):109. doi: 10.1186/s13068-025-02703-9.

ABSTRACT

BACKGROUND: Liquid fuels from lignocellulosic feedstocks are required for transition to a sustainable bioeconomy. However, the recalcitrance of carbon-containing feedstock cell walls to deconstruction poses a barrier to cost effective biological conversion of plant biomass to biofuels. One-step consolidated bioprocessing (CBP) in which anaerobic thermophilic bacteria convert lignocellulosic biomass into liquid fuels is a platform for overcoming the recalcitrance of plant biomass.

RESULTS: The amounts of hemicellulosic and pectic polysaccharides, two complex cell wall glycans that contribute to plant biomass recalcitrance and that are partially solubilized during CBP of switchgrass aerial biomass by Clostridium thermocellum were evaluated in the liquor, solid residues and residue washate recovered during a 120-h CBP process. After 120 h, 24% of milled switchgrass was solubilized in the C. thermocellum CBP platform. Higher concentrations of arabinose, xylose, galactose, and glucose accumulated in the CBP-fermentation liquor and washate compared to fermentation controls without C. thermocellum, indicating that C. thermocellum solubilized hemicelluloses, but did not fully metabolize them. After five days of fermentation, the relative amount of rhamnose in the solid residues increased by 16% compared to controls, and CBP solid residues had more than 23% increased reactivity against RG-I reactive monoclonal antibodies, indicating that the pectic polymer rhamnogalacturonan I (RG-I) was not effectively solubilized from switchgrass biomass by C. thermocellum CBP. Similarly, the amount of mannose (Man) in the CBP solid residues increased by 7% and reactivity against galactomannan reactive antibodies increased by greater than 14%, indicating that the hemicellulosic polymer galactomannan was also resistant to degradation by C. thermocellum during CBP fermentation.

CONCLUSIONS: These findings show that C. thermocellum is unable to effectively degrade RG-I pectic and galactomannan hemicellulosic components in switchgrass biomass. Targeting these polymers for improved solubilization could enhance the efficiency of conversion of grass biomass to biofuels.

PMID:41146239 | DOI:10.1186/s13068-025-02703-9

Commun Mater. 2025;6(1):34. doi: 10.1038/s43246-025-00749-8. Epub 2025 Feb 22.

ABSTRACT

Because proteins do not efficiently pass through the plasma membrane, protein therapeutics are limited to target ligands located at the cell surface or in serum. Lipid nanoparticles can facilitate delivery of polar molecules across a membrane. We hypothesized that because most proteins are amphoteric ionizable polycations, proteins would associate with anionic lipids, enabling microfluidic chip assembly of stable EP-LNPs (Encapsulated Proteins in Lipid NanoParticles). Here, by employing anionic lipids we were able to efficiently load proteins into EP-LNPs at protein:lipid w:w ratios of 1:20. Several proteins with diverse molecular weights and isoelectric points were encapsulated at efficiencies of 70 75%-90% and remained packaged for several months. Proteins packaged in EP-LNPs efficiently entered mammalian cells and fungal cells with cell walls. The proteins delivered intracellularly were functional. EP-LNPs technology should improve cellular delivery of medicinal antibodies, enzymes, peptide antimetabolites, and dominant negative proteins, opening new fields of protein therapeutics.

PMID:41146908 | PMC:PMC12553553 | DOI:10.1038/s43246-025-00749-8

J Exp Bot. 2025 Oct 28:eraf471. doi: 10.1093/jxb/eraf471. Online ahead of print.

ABSTRACT

Climate change is rapidly modifying environmental conditions for plant-microbe interactions. Extreme climate conditions and altered climate patterns have increased the frequency and severity of plant disease outbreaks worldwide, posing a major threat to global food security. Climate-related stress affects host-microbe interactions by modulating plant immunity and pathogen virulence. Understanding how plants perceive and respond to thermal stresses, and how this intersects with disease resistance mechanisms, is essential for mitigating future crop losses. This review synthesizes current knowledge on the molecular and cellular basis of temperature sensing, its effects on immune signaling and cell biology in model plant Arabidopsis. Advancing our understanding of these interactions is critical for developing climate resilient crops capable of withstanding the complex stresses.

PMID:41147144 | DOI:10.1093/jxb/eraf471

Biotechnol Biofuels Bioprod. 2025 Oct 22;18(1):108. doi: 10.1186/s13068-025-02704-8.

ABSTRACT

BACKGROUND: Plant-based materials have the potential to replace some petroleum-based products, offering compostability and biodegradability as critical advantages. Xylan-rich biomass sources are gaining recognition due to their abundance and underutilization in current industrial applications. Research of potential xylan applications has been complicated by the complex and heterogeneous structure that varies for different xylan feedstocks. Acylation is a broadly used reaction in functionalization of polysaccharides at an industrial scale. However, the efficiency of this reaction varies with the xylan source. To optimize xylan valorization, a systematic understanding of structure-reactivity relationships is essential.

RESULTS: This study explores, characterizes, and compares various xylan feedstocks in the acylation process. Xylan feedstocks were analyzed for their chemical composition, degree of polymerization, branching, solubility, and presence of impurities. These features were correlated with xylan glycotypes’ reactivity toward functionalization with succinic anhydride in an optimized DMSO/KOH condition, achieving carboxyl contents of up to 1.46. We used principal component analysis and hierarchical clustering to identify key structural features of xylan that promote its reactivity. Our findings reveal that xylans with higher xylose content and lower degrees of branching exhibit enhanced reactivity, achieving higher carboxyl content and yields. Structural analyses confirmed successful modification, and light scattering analyses showed dramatic changes in the solution properties. Succinylation improves the solubility and film-forming properties of native xylans.

CONCLUSIONS: This study shows key structure-reactivity relationships in xylan succinylation, establishing that low branching, high xylose content, and reduced lignin impurity enhance chemical functionalization. The results offer a framework for selecting optimal biomass feedstocks and support future efforts in genetic and synthetic biology to design plants with tunable xylan architectures. These findings advance the hemicellulose valorization for applications in coatings and packaging.

PMID:41126303 | DOI:10.1186/s13068-025-02704-8

G3 (Bethesda). 2025 Oct 23:jkaf253. doi: 10.1093/g3journal/jkaf253. Online ahead of print.

ABSTRACT

Solanum microdontum Bitter is a diploid wild Andean relative of potato that has shaped the domestication and adaptation of modern cultivated potato to diverse environments. Solanum microdontum has the potential to provide a wealth of untapped genetic material for use in addressing current challenges in potato breeding. Here, we report a high-quality 772 Mb reference genome sequence for S. microdontum that is anchored to 12 chromosomes. The resulting genome assembly has 99.0% complete Benchmarking Universal Single Copy Orthologs and an N50 scaffold length of over 57 Mb, indicating a high level of completeness. Annotation of the assembly resulted in the identification of 37,324 protein coding genes and 65% repetitive sequence. A total of 1,187 nucleotide-binding leucine-rich repeat genes were predicted from the assembly, of which 93.1% overlapped an annotated high-confidence gene model. A k-mer based kinship matrix derived from a 107-member S. microdontum diversity panel revealed an underlying population structure that corresponds to geographic proximity. The S. microdontum dataset enhances publicly available potato genome resources by providing breeders with genetic, molecular, and germplasm resources for newly developed diploid potato breeding programs.

PMID:41128648 | DOI:10.1093/g3journal/jkaf253

Plant Dis. 2025 Oct 21. doi: 10.1094/PDIS-05-25-1023-RE. Online ahead of print.

ABSTRACT

Maize, a globally important staple crop, faces significant yield losses due to corn smut disease, caused by the fungal pathogen Ustilago maydis. Most cultivated maize lines lack genetic resistance, necessitating the identification of new resistance sources. This study evaluated resistance to U. maydis across diverse maize germplasm, including four maize inbred lines (B73, H95, Mo17, and Golden Bantam), three teosinte accessions (Zea mays ssp. parviglumis, Z. mays ssp. luxurians, and Z. mays ssp. diploperennis), and two maize-teosinte near-isogenic lines (NILs). Phenotypic resistance was assessed at the seedling and reproductive growth stages (ear and tassel) 7-, 10-, 14-, and 21-days post-inoculation with U. maydis at four inoculum concentrations. At the seedling stage, teosinte accessions demonstrated resistance to U. maydis, while maize inbreds showed varying levels of susceptibility. The maize-teosinte NILs had better resistance than maize genotypes at the seedling and reproductive stages, with up to 75% fewer ear/tassel galls and 65% less area under the disease progress curve. This enhanced resistance likely stems from introgressed teosinte genomic segments, particularly a 3.9 Mbp region on chromosome 9. Resistance differed across developmental stages and exhibited dose-dependent responses to inoculum concentration. These results suggest that resistance to U. maydis is based on genotype, developmental stage, and dose-dependent genetic resistance. The maize-teosinte NILs have genes associated with resistance to U. maydis that were derived from the teosinte parent, suggesting maize-teosinte NILs and teosinte are valuable genetic resources for enhancing U. maydis resistance in cultivated maize.

PMID:41117632 | DOI:10.1094/PDIS-05-25-1023-RE

Ecol Appl. 2025 Oct;35(7):e70125. doi: 10.1002/eap.70125.

ABSTRACT

The misalignment of species adaptations with current environmental conditions can cause ecosystems to lose resilience, accumulate resilience debt, and transition to another state. Such a state change is evident in eastern North American broadleaf forests where dominant tree species are shifting from oaks (Quercus spp.) to mesophytic species such as maples (Acer spp.). The replacement of oaks is widespread and threatens the ecosystem services these forests provide, generating interest in using forest management to halt or reverse this change. The national Fire and Fire Surrogate (FFS) study was a large-scale study of forest management practices, and the Green River FFS site in western North Carolina (initiated in 2001) offers the opportunity to understand how management actions affect oak forest resilience. The Green River FFS site implemented three experimental treatments replicated across three spatial blocks: mechanical felling of saplings and ericaceous shrubs (Mech), prescribed fire (Fire), and a combination (Mech + Fire), which were compared to untreated controls (Control). Here, we used this long-running experiment to evaluate oak forest resilience by examining changes in overstory basal area and forest composition among overstory trees, saplings, and seedlings. We found that basal area increased in the Control and Mech treatments, was unchanged in the Fire treatment, and decreased in the Mech + Fire treatment as a result of mortality. Oak sapling abundances increased with reduced basal area, a pattern not found with the major mesophytic representative, maples. This suggests that oaks are well positioned to recruit to the overstory where basal area has decreased due to overstory mortality, and at the Green River FFS site, this was best achieved in the Mech + Fire treatment. Creating conditions where oak saplings have an advantage over maples requires the mortality of some overstory trees, including desirable oaks. Taken together, our findings suggest that the misalignment of oak traits and current environmental conditions has led to resilience debt, which may be reduced when management actions mimic a severe disturbance that results in the opening of the canopy. Thus, management actions that combine mechanical felling and repeated prescribed fires may promote sustained oak dominance in the future.

PMID:41111267 | DOI:10.1002/eap.70125