Author: slquinlan

Microb Genom. 2026 Oct;12(10). doi: 10.1099/mgen.0.001868.

ABSTRACT

Campylobacter jejuni is a leading cause of foodborne illness worldwide, yet infection sources are not always clear. We used whole-genome sequencing to compare C. jejuni from bird faeces collected in cherry orchards in Michigan to 214 clinical isolates from Michigan patients and 1,286 published bird-derived C. jejuni genomes. The bird isolates from Michigan possess class D β-lactamases and multiple virulence genes and belong to seven sequence types (STs), including three novel STs. Two isolates obtained from different bird species differed by only a single core-genome SNP despite being collected on different days, while a genetically similar lineage was observed in American robins sampled a year apart. Although the bird- and human-derived strains cluster within a core gene phylogeny, they differ by >4,000 core-genome SNPs. Relative to 1,286 genomes, Michigan bird isolates do not form a single cluster but are distributed throughout the core gene multilocus sequence typing tree. Analysis of shared STs identified genomes from dogs, water, chickens and human clinical infections that differ from Michigan bird isolates by only 10-38 core-genome SNPs. These findings demonstrate that Michigan birds harbour diverse C. jejuni lineages, with some belonging to widely distributed genotypes that are related to isolates from different bird species, host types and geographic locations. Although the substantial genomic separation between Michigan bird and human isolates indicates that they are not related, they were collected during different time periods and geographic locations, thereby limiting our ability to make comparisons. Improving understanding of the diversity, host range and transmission dynamics of wildlife-associated C. jejuni lineages is critical for strengthening source attribution studies and guiding food safety policy in agroecosystems.

PMID:42909482 | DOI:10.1099/mgen.0.001868

Front Plant Sci. 2026 Oct 5;17:1935720. doi: 10.3389/fpls.2026.1935720. eCollection 2026.

ABSTRACT

Winter wheat is grown worldwide primarily for grain, yet it also serves as an important cool-season forage, supporting livestock production when other feed is scarce. Wheat can be utilized as grazed pasture or harvested as hay, silage, and straw, and is widely used as dual-purpose (forage + grain) and double-cropping systems. During vegetative growth, wheat forage is highly palatable and nutritive, typically containing 20-30% crude protein (CP), and >80% digestibility, supporting rapid liveweight gains in beef cattle. However, forage quality is highly dynamic: as wheat matures, CP and energy decline, while neutral detergent fiber (NDF), acid detergent fiber (ADF), and lignin increase, reducing intake potential and digestibility. Forage quality is also affected by moisture, fertilization, and wheat class. At comparable developmental stages, winter and spring wheat generally show little inherent differences in forage quality, indicating that maturity and management are the major determinants of quality. This review synthesizes current knowledge on wheat forage in dual-purpose and grazing systems, emphasizing dry matter, CP, NDF, ADF, acid detergent lignin, relative feed value, and relative forage quality as key indicators of biomass, nutritive value, intake potential, and digestibility. We further assess developmental shifts in these traits and their consequences on livestock intake, animal performance, and grazing management, together with forage evaluation methods such as near-infrared reflectance spectroscopy. We also examine genetic and genomic approaches for improving forage traits. Wheat breeding has historically prioritized grain yield and straw characteristics, genomic dissection of forage quality remains limited. Nevertheless, recent genome-wide association, QTL mapping, and genomic selection studies targeting water-soluble carbohydrates, fiber fractions, and digestibility-related traits highlight promising avenues for improvement. Overall, wheat forage can provide exceptionally valuable winter feed resources, but its quality is governed by strong developmental, environmental, and genetic effects. Improved screening methods and breeding targets, such as combining high protein and energy with agronomic resilience, are needed to exploit wheat’s dual-purpose potential. This review integrates agronomic, animal nutrition, and genetic perspectives to guide future research and breeding of high-quality forage wheat.

PMID:42899183 | PMC:PMC13679537 | DOI:10.3389/fpls.2026.1935720

Mol Plant. 2026 Oct 19:S1674-2052(26)00347-3. doi: 10.1016/j.molp.2026.10.008. Online ahead of print.

ABSTRACT

Adaptive evolution contributes to species diversification and reproductive success, which is a central focus of evolutionary biology. Elucidating the underlying mechanisms is crucial for understanding how plants respond to changing environments. Recent sequencing advances have generated vast plant genomic data, enabling evolutionary analyses at unprecedented phylogenetic depth and molecular resolution. Here, we survey the landscape of sequenced plant genomes, summarize recent advances in sequencing technologies and assembly methods, and synthesize how genomic variants are detected through micro- and macro-evolutionary analyses and how their fates are shaped by distinct modes of selection. We then highlight several major forms of genomic variation and their potential contributions to adaptive evolution, including structural variants, transposable element activity, and whole-genome duplications. We further survey the associated genomic signatures of extremophiles and plant terrestrialization as frameworks for understanding diverse and compound environmental stresses. Finally, we discuss emerging genomic research trends and future directions, which aim to deepen insights into the evolutionary architecture of plant genomes and provide a theoretical foundation for crop improvement, ecological conservation, and biotechnological applications.

PMID:42897846 | DOI:10.1016/j.molp.2026.10.008

G3 (Bethesda). 2026 Oct 10:jkag278. doi: 10.1093/g3journal/jkag278. Online ahead of print.

ABSTRACT

Southern stem canker (SSC), caused by Diaporthe aspalathi, is a major soybean disease causing yield losses of up to 80%. Genetic resistance is the most effective and sustainable strategy for managing SSC. “Tracy-M” is a cultivar with broad resistance to D. aspalathi isolates; however genomic location of the resistance is unknown. To determine the genetic basis of SSC resistance in Tracy-M and its derived progeny, two Tracy-M-derived lines, D85-10404 and D85-10412, were each crossed with a common susceptible parent, G81-2057, to develop recombinant inbred line (RIL) populations. Quantitative Trait Locus (QTL) sequencing (QTL-seq) and composite interval mapping (CIM) identified a common major QTL on chromosome (Chr) 2 in both lines corresponding to Rdm1 locus defined from a previous genetic study. Additionally, second QTL located on Chr 17 (Rdm2 locus) was only detected in the D85-10412-derived RIL population. To validate Tracy-M-derived resistance, an F2:3 population from G00-3213 × Tracy-M was developed. Bulked segregant analysis (BSA) and CIM identified a major QTL on Chr 14, overlapping the previously reported Rdm3 locus in “Crockett” and PI 398469, while Rdm1 was not detected, suggesting genetic background effects. Kompetitive allele-specific PCR (KASP) markers were developed to facilitate selection of Rdm1, Rdm2, and Rdm3 resistance alleles in soybean breeding programs.

PMID:42857980 | DOI:10.1093/g3journal/jkag278

bioRxiv [Preprint]. 2026 Sep 7:2026.09.03.748874. doi: 10.64898/2026.09.03.748874.

ABSTRACT

Plant-parasitic nematodes cause extensive crop losses that threaten global food security and create substantial economic hardship, yet strategies for their control remain limited. Although plant-parasitic nematodes have life cycles that mirror those of their free-living and animal-parasitic relatives, comparatively little is known about the signals that drive life-cycle progression. Dafachronic acids (DAs) are steroid hormones that control life cycle by activating DAF-12 nuclear receptors in Caenorhabditis elegans and animal-parasitic nematodes. To define whether an analogous pathway exists in plant-parasitic nematodes, we investigated the responsiveness of DAF-12 orthologs from six plant-parasitic nematode species to Δ7-DA, an endogenous DAF-12 ligand in C. elegans and several animal-parasitic nematodes. We find that whereas some plant-parasitic nematode receptors are activated by Δ7-DA, others are not. Structural modeling of all six ligand-binding domains, together with docking of Δ7-DA into each model, indicates that responsiveness is governed by a combinatorial ligand-recognition network surrounding the ligand carboxylate rather than by any single contact residue. We further demonstrate that egg and second-stage juvenile extracts from the soybean cyst nematode, Heterodera glycines, lack detectable DA but contain distinct lipophilic fractions that activate its DAF-12 ortholog. Together, these findings suggest that many plant-parasitic nematodes utilize endogenous DAF-12 ligands that are structurally distinct from DA. Uncovering modulators of this pathway could lead to new strategies to combat nematode-driven crop loss.

PMID:42818229 | PMC:PMC13622478 | DOI:10.64898/2026.09.03.748874

Appl Environ Microbiol. 2026 Oct 7:e0125726. doi: 10.1128/aem.01257-26. Online ahead of print.

ABSTRACT

Maize produces pre-formed secondary metabolites with antimicrobial and invertebrate anti-herbivory properties. Fusarium verticillioides, a mycotoxigenic maize pathogen, detoxifies the maize phytoanticipin 2-benzoxazolinone (BOA) through gene action of FvMBL1, which encodes a putative metallo-β-lactamase within the FDB1 gene cluster. This cluster is also present in other maize-colonizing fungi, including the pathogen Colletotrichum graminicola and, as reported here, the protective endophyte Sarocladium zeae, which exhibits antagonistic activity against mycotoxigenic fungi. The role of the FvMBL1 ortholog in S. zeae, designated SzMBL1, was assessed by gene deletion and add-back complementation. Deletion of SzMBL1 rendered S. zeae incapable of degrading BOA and therefore unable to grow on BOA-amended medium, whereas complemented add-back strains restored BOA tolerance and, in some cases, enhanced growth at higher concentrations of BOA. Quantitative PCR analyses revealed higher copy numbers and expression levels in all add-back transformants relative to the wild type, consistent with their enhanced growth. HPLC-MS/MS analysis further showed that SzMBL1 hydrolyzes BOA, ultimately resulting in biotransformation into the non-toxic metabolite N-(2-hydroxyphenyl)malonamic acid (HPMA). Together, this study confirms the conserved function of the SzMBL1 gene involved in BOA detoxification. This study suggests that the FDB1 gene cluster, harboring SzMBL1 in S. zeae, was likely transferred through horizontal gene transfer between maize-colonizing fungi and plays a role in the degradation of host-derived secondary metabolites that function as filters limiting which fungi are most frequently associated with maize.IMPORTANCEMaize produces secondary metabolites such as 2-benzoxazolinone (BOA) to help protect against microbes and insects. The pathogenic Fusarium verticillioides carries FvMBL1, a gene within the FDB1 gene cluster that helps break down BOA. This cluster is also present in other maize-associated fungi such as Colletotrichum graminicola and, as reported here, the protective fungus Sarocladium zeae. In our experiments, when a gene similar to FvMBL1, denoted SzMBL1, is deleted in S. zeae, the fungus could no longer break down BOA or grow on BOA-amended medium. Complementation restored BOA tolerance and growth phenotypes. Notably, some S. zeae add-back strains showed increased growth at higher BOA concentrations. Our analysis showed that these hypertolerant complemented strains had multiple, transcriptionally active copies of SzMBL1. The study highlights the role of SzMBL1 in BOA detoxification, thereby aiding fungal tolerance to antimicrobial compounds, and supports the hypothesis that the FDB1 gene cluster can be horizontally transferred among maize-colonizing fungi.

PMID:42841629 | DOI:10.1128/aem.01257-26

PLoS Genet. 2026 Oct 5;22(10):e1012327. doi: 10.1371/journal.pgen.1012327. Online ahead of print.

ABSTRACT

In animals, plants, and some fungi, Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) to establish transcriptionally repressed chromatin. Here, we identify the histone acetyltransferase RTT109 as a key regulator of PRC2-repressed domains in the model fungus Neurospora crassa. Although RTT109 interacts with the Vps75 homolog Nucleosome Assembly Factor 2 (NAF-2), we show that proper structure and function of PRC2-methylated chromatin require RTT109 catalytic activity but are independent of NAF-2 and H3K56 acetylation. We further demonstrate that H3K27me3 can be stably propagated over multiple rounds of mitosis in the absence of sequence-specific PRC2 targeting, and that RTT109 is essential for maintenance of the repressed state. These findings uncover a replication-linked mechanism for epigenetic memory and establish RTT109 as a key regulator of Polycomb-mediated chromatin inheritance.

PMID:42832562 | DOI:10.1371/journal.pgen.1012327

Proc Natl Acad Sci U S A. 2026 Oct 6;123(40):e2524371123. doi: 10.1073/pnas.2524371123. Epub 2026 Sep 29.

ABSTRACT

Many motile and sensory functions of cilia and flagella depend on the precise localization of transmembrane proteins within the ciliary membrane. Rather than being uniformly distributed, these proteins are often targeted to specific subciliary regions along the length or circumference of cilia. Here, we use genome editing and in vivo imaging to dissect the spatial organization of the channel protein PKD2 in Chlamydomonas cilia. MST3, a PKD2-like protein with five transmembrane helices (5TMH), is localized exclusively to the distal cilium, where it is essential for the localization of PKD2 and the formation of the hair-like mastigonemes. MST3, however, is dispensable for PKD2 assembly in the proximal cilium. In contrast, the PKD2-like 5TMH protein Proximal PKD2 Interactor (PPI) resides in the proximal cilium, where it is required for PKD2 assembly; ppi mutants retain distal PKD2 and mastigonemes. In mst3 ppi double knockouts, both proximal and distal PKD2 are absent, revealing that MST3 and PPI organize PKD2 into distal and proximal regions. Further, PKD2 colocalizes and comigrates with PKD2-like protein 1 (PLP1), another 5TMH protein, in cilia, indicating that they are present together in a complex. While plp1 mutants swim largely normally, mst3 and, to a lesser degree, ppi mutants swim with reduced velocity, indicating a functional specialization of the different ciliary PKD2 complexes. Thus, Chlamydomonas PKD2 associates with one of several 5TMH proteins to form spatially and genetically distinct PKD2 complexes, while also establishing their longitudinal distribution in cilia.

PMID:42809393 | DOI:10.1073/pnas.2524371123

G3 (Bethesda). 2026 Sep 28:jkag269. doi: 10.1093/g3journal/jkag269. Online ahead of print.

ABSTRACT

Polyploidization in peanut (Arachis hypogaea L.) fixed heterosis but also caused a genetic bottleneck isolating cultivated peanut from its wild diploid relatives. Mechanisms such as homoeologous exchange can partially restore genetic diversity by generating new allelic combinations. Double reduction is a rare polyploid-specific segregation pattern in which a single-dosage locus yields duplex gametes. It requires multivalent formation-associated with homoeologous exchange in allopolyploids-and crossing over between non-sister chromatids. Although peanut mainly exhibits disomic pairing, occasional multivalents theoretically allow low-frequency double reduction. To estimate double reduction and examine its relationship with genetic instability, we constructed a high-density phased linkage map (9,717 markers, 0.22 cM average spacing) from a backcross population between cultivated peanut and the neoallotetraploid [A. magna × A. stenosperma]4x (MagSten). Initial maps showed distinctive double linkage group artifacts, and some progenies displayed abnormal genotyping patterns linked to unbalanced chromosomal compositions, outcomes of homoeologous exchange. Removing these progenies resolved the artifacts, revealing a previously unrecognized mapping artifact in allotetraploid peanut and suggesting a common origin for similar artifacts observed in other linkage maps. Analysis of the phased map detected double reduction in 12% of progenies; one event was confirmed as producing a genomic composition matching theoretical predictions, supporting the hypothesis that double reduction causes unbalanced genomic compositions in allopolyploids as well. These results indicate that double reduction is a rare but recurrent phenomenon in segmental allotetraploid peanut that, together with homoeologous exchange, contributes to genetic instability and generates new allelic combinations in this and likely other allopolyploid genomes.

PMID:42802945 | DOI:10.1093/g3journal/jkag269

Phytopathology. 2026 Sep 26. doi: 10.1094/PHYTO-07-26-0235-R. Online ahead of print.

ABSTRACT

Fusarium head blight (FHB) is a destructive disease of wheat and barley caused by a complex of Fusarium species, including Fusarium poae. However, the transcriptional responses of F. poae during spike colonization remain insufficiently characterized. This study aimed to characterize and compare the temporal transcriptomic responses of F. poae during barley and wheat spike infection. We profiled the in planta transcriptome of F. poae isolate GA18W 5.2.4 in barley cv. Stander and wheat cv. SS8641 at 0, 24, 48, 72, and 96 h after inoculation (HAI). RNA sequencing, differential expression analysis, functional enrichment, and evidence-supported protein annotation characterized temporal and host-associated transcriptional patterns. Likelihood ratio tests identified 7,852 time-responsive genes in barley and 5,464 in wheat. Relative to 0 HAI, 2,858 to 3,868 genes were upregulated in barley and 1,631 to 3,921 in wheat, whereas downregulated genes were uncommon. Shared upregulated genes increased from 1,410 at 24 HAI to 3,192 at 96 HAI. Upregulated genes in both hosts were enriched for protein synthesis, energy metabolism, intracellular transport, and protein homeostasis. Curated DEG categories comprised candidates representing cell wall-degrading enzymes, effectors, biosynthetic gene cluster core genes, transcription factors, transporters, signaling proteins, and stress/detoxification proteins. Many categories were represented earlier or more broadly in barley but increased later in wheat, with several approaching or exceeding barley by 96 HAI. These findings reveal a shared core transcriptional program with host-associated temporal differences and provide a basis for further prioritization and functional validation of candidate genes involved in F. poae colonization and FHB development.

PMID:42799990 | DOI:10.1094/PHYTO-07-26-0235-R