Category: Pub Med

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

Theor Appl Genet. 2026 Sep 27;139(10):282. doi: 10.1007/s00122-026-05381-9.

ABSTRACT

Crockett and PI 398469 carry distinct resistance alleles at the Rdm3 locus for soybean southern stem canker, supported by progeny analysis, sequence variation, candidate gene expression profiling, and allele transmission patterns. Genetic resistance to southern stem canker (SSC) in soybean is predominantly conditioned by the Rdm3 locus on chromosome (Chr) 14. Resistance at this locus has been identified in ‘Crockett’ and PI 398469; however, the allelic relationship between these lines remains unresolved. This study aimed to determine whether SSC resistance in Crockett and PI 398469 is governed by the same or distinct alleles at the Rdm3 locus. Progeny analysis of a Crockett × PI 398469 recombinant inbred line (RIL) population identified recombinant lines with weaker resistance and broader phenotypic variation than either parent, indicating that recombination at the Rdm3 locus disrupted favorable allele combinations and generated unexpected SSC resistance phenotypes. Consistent with this, sequence analysis of two priority candidate genes, Glyma.14G023500 and Glyma.14G022600, revealed variation associated with resistance between Crockett and PI 398469, as well as among resistant and susceptible RILs. Expression profiling of these candidate genes further demonstrated genotype-dependent temporal patterns, suggesting distinct regulatory mechanisms underlying resistance conferred by Rdm3 alleles from Crockett and PI 398469. In addition, the resistance alleles differed in their transmission behavior, with segregation distortion and underrepresentation of the Crockett allele observed across breeding populations and germplasm pools. Pedigree analysis further indicated an atypical origin of the Crockett Rdm3 allele. These results demonstrate that Crockett and PI 398469 carry functionally distinct resistance alleles at Rdm3, confirming allelic variation at a major SSC resistance locus and providing insight into the effective deployment of Rdm3 resistance in soybean breeding.

PMID:42801351 | DOI:10.1007/s00122-026-05381-9

Plant Dis. 2026 Sep 22. doi: 10.1094/PDIS-03-26-0441-RE. Online ahead of print.

ABSTRACT

Native plant restoration efforts in California are continuously challenged by Phytophthora-induced diseases, particularly through nursery introductions, resulting in significant losses and distribution of pathogens into restoration areas. Effective diagnostic strategies can help manage Phytophthora, yet determining the most suitable method, considering specificity, sampling time, resource availability, and expertise, remains uncertain. This study compares the effectiveness of five diagnostic methods: irrigation leachate baiting, ImmunoStrip® for Phytophthora, culture-based isolations, recombinase polymerase amplification (RPA, targeting genus-specific trnM-trnP-trnM locus), and quantitative polymerase chain reaction (qPCR, targeting genus-specific atp9-nad9 locus) on artificially inoculated and on naturally infested ornamental plants. For artificially inoculated plant testing, two native California ornamentals, Frangula californica and Heteromeles arbutifolia, were inoculated with three Phytophthora species: P. cinnamomi, P. cactorum, and P. cryptogea, and sampled three times, every six weeks post-inoculation. The sampled plants, along with the non-inoculated controls, were subjected to the five detection methods for Phytophthora detection. Among the detection assays, RPA, qPCR, and irrigation leachate baiting had the highest Phytophthora detection rates, regardless of the host, sampling time, or pathogen species (P < 0.01). For naturally infested plants, molecular assays consistently detected Phytophthora from three horticultural and two native nurseries (one accredited through Accreditation to Improve Restoration (AIR) program and other in process), with a subset of samples independently validated by another laboratory. The AIR-certified nursery showed no Phytophthora and the lowest detection probability across methods. These results indicate that implementing strategic detection approaches, combined with best management practices, can improve detection and prevent Phytophthora spread to wildlands.

PMID:42771457 | DOI:10.1094/PDIS-03-26-0441-RE

Ecology. 2026 Sep;107(9):e70525. doi: 10.1002/ecy.70525.

ABSTRACT

The distributions of rare species are often estimated from presence-absence data, but undetected occurrences (imperfect detection) can lead to consequential underestimates of occupancy. Despite its standard use in animal ecology, detection probability (p) is rarely incorporated into plant occupancy estimates. Plants with cryptic life stages or traits (e.g., seed banks, dormancy) may be especially prone to periods of unobservability, resulting in imperfect detection even when a species is present. We tested the hypothesis that cryptic traits lower detection by reviewing published estimates of p in plant systems. While taxa with cryptic traits, particularly annual plants with seed banks and deciduous geophytes, exhibited lower p, there was wide variation across genera and publications. We then conducted a case study of the rare, annual, aquatic plant, Gratiola amphiantha (snorkelwort), endemic to ephemerally rain-filled granite rock outcrop pools, to estimate occupancy (Ψ), p, and their environmental drivers. We found that Ψ increased with deeper soils and larger pool areas. Snorkelwort exhibited a high but imperfect p (mean p = 0.87) that varied with competing vegetation cover and census date. Modeling Ψ across varying levels of survey effort showed that ignoring imperfect detection can underestimate total occupancy estimates by up to 43%; however, our empirical p estimates indicate a minimum of just two surveys can reach 95% detection for snorkelwort. Our findings demonstrate that imperfect detection is an important and underappreciated limitation in plant occupancy studies, even for species with high detection probability. For rare plants, explicitly incorporating taxon-specific p estimates and marginally increasing survey effort can substantially improve the accuracy of occupancy models.

PMID:42775469 | DOI:10.1002/ecy.70525

Plant Dis. 2026 Sep 21. doi: 10.1094/PDIS-05-26-0927-FE. Online ahead of print.

ABSTRACT

Bacterial leaf spot (BLS) is one of the most destructive diseases of pepper (Capsicum spp.) worldwide, causing significant yield and quality losses under warm and humid conditions. The disease is caused by multiple Xanthomonas species, whose rapid evolution continues to challenge effective management. This review synthesizes current knowledge on BLS in pepper, including pathogen taxonomy, global distribution, and the historical progression of disease research and resistance breeding. We summarize advances in the identification and deployment of resistance loci, including major race-specific genes, as well as recessive resistance genes and quantitative resistance sources, and highlight the development of molecular markers supporting resistance breeding programs. We further integrate findings from transcriptomic, proteomic, metabolomic, and microRNA (miRNA) studies to elucidate the multilayered defense responses of pepper to Xanthomonas infection. Collectively, these multi-omics approaches indicate that effective resistance is governed by coordinated regulation of defense signaling pathways (e.g., salicylic acid, jasmonic acid, and ethylene), activation of resistance genes (including Bs2, Bs3, and related loci such as bs5 and bs6) and defense-associated transcription factors (e.g., WRKY), differential accumulation of defense-related proteins involved in stress responses, and metabolic reprogramming involving secondary metabolites. Finally, we outline key knowledge gaps and future priorities for developing durable and broad-spectrum resistance to BLS in pepper.

PMID:42766675 | DOI:10.1094/PDIS-05-26-0927-FE

Plant Genome. 2026 Sep;19(3):e70306. doi: 10.1002/tpg2.70306.

ABSTRACT

Switchgrass (Panicum virgatum L.) improvement requires selection methods that remain effective across environments. Biomass yield is strongly influenced by genotype-by-environment (G × E) interaction. We evaluated genomic prediction models for biomass yield, spring emergence (SE), and flowering time (FT) in half-sibs at three southeastern US locations (Watkinsville, GA; Tifton, GA; and Knoxville, TN). Predictive performance was assessed within each site-year using five-fold cross-validation, comparing a parental general combining ability (GCA) baseline with Bayesian models, genomic BLUP (GBLUP), and a dominance model (GBLUPD). We further quantified the sensitivity of yield prediction to single-nucleotide polymorphism (SNP) density. Predictive abilities as Pearson correlation coefficient (PCC) increased as the SNP number rose from the minimum of 100 to 2500-5000 SNPs, with only minimal gains observed up to 10,000 SNPs and beyond. Genomic models consistently outperformed parental GCA baseline for yield, with the highest PCC of 0.45-0.55 in 2022 for Georgia, followed by declines (PCC = 0.25-0.35) in 2024. This indicated stronger G × E (where E represents combined year-location) impacts on mature switchgrass stands. FT showed higher predictive ability than yield, with PCC > 0.50 in Georgia and PCC > 0.28-0.33 in Tennessee. SE exhibited intermediate-to-high PCC of 0.65-0.70 in Georgia during 2022-2023 and a PCC of 0.45-0.47 in Tennessee. The GBLUPD provided small repeatable gains for yield and SE in comparison to GBLUP. FT exhibited genetic correlations exceeding 0.90 at Knoxville, which showed it as a transferable predictor for multi-environment selection. Collectively, these results indicate that modest SNP sets can be sufficient for yield prediction and highlight environment-dependent model performance.

PMID:42765369 | DOI:10.1002/tpg2.70306

mBio. 2026 Sep 21:e0205126. doi: 10.1128/mbio.02051-26. Online ahead of print.

ABSTRACT

Cryptococcus neoformans is an opportunistic fungal pathogen responsible for approximately 20% of deaths in patients with HIV/AIDS. Adaptation to host physiological conditions, including high CO₂, is required for infection. We discovered that an uncharacterized protein with an RNA-binding domain, Psc1, functions as a basidiomycete-specific suppressor of the kinase mutant cbk1Δ and partially rescues its growth defect in high CO₂. Psc1 contains multiple consensus cell wall biosynthesis kinase 1 (Cbk1) phosphorylation sites that are required for maintenance of CO₂ fitness. We hypothesized that, in the absence of Cbk1, Psc1 negatively regulates CO₂ tolerance by binding to and interfering with the function of mRNAs required for CO₂ tolerance. Supporting this model, we found that multiple mRNAs that are required for CO₂ tolerance associate with Psc1 in the absence of Cbk1. Furthermore, the transcripts of ZDS3, a gene required for CO₂ tolerance, predominantly colocalize with Psc1, which forms condensates in the cbk1Δ mutant at high CO₂, correlating with impaired growth. Collectively, our findings support the conclusion that C. neoformans adapts to high CO₂ through a post-transcriptional mechanism where Cbk1 phosphorylates Psc1, preventing its binding to, and subsequent functional inhibition of, mRNAs important for CO₂ tolerance.IMPORTANCEHigh CO₂ is growth-inhibitory, and therefore adaptation to high CO₂ stress is a universal cellular phenomenon required for survival. The environmental fungus, Cryptococcus neoformans, encounters high CO₂ environments in the host, and thus tolerance to high CO₂ is critical for its ability to cause lethal infections. The regulation of Ace2p and morphogenesis (RAM) pathway is required for its growth in high CO₂. We found that CO₂ tolerance is mediated post-transcriptionally by a downstream target of the RAM pathway, the RNA-binding protein Psc1. In the absence of the RAM pathway, Psc1 sequesters mRNA transcripts required for growth in high CO₂, preventing growth. These findings reveal a previously uncharacterized post-transcriptional regulatory mechanism that controls cryptococcal adaptation to high CO₂.

PMID:42765704 | DOI:10.1128/mbio.02051-26

NAR Genom Bioinform. 2026 Sep 15;8(3):lqag107. doi: 10.1093/nargab/lqag107. eCollection 2026 Sep.

ABSTRACT

Genomic DNA encodes regulatory information that determines where, when, and to what extent genes are expressed. Theoretically, we should be able to identify these transcriptional “instructions” by examining genomic DNA sequence alone, yet this has remained challenging. Here we present the Vertebrate Regulatory MOdule Detector (VRMOD), a method that accurately predicts gene regulatory sequences using only the query genomic sequences. We applied VRMOD to 309 Ensembl genomes, generating a compendium of high-resolution, genome-position-fixed cis-regulatory modules without parameter tuning. We performed extensive computational evaluation and experimental validation of VRMOD predictions. Notably, VRMOD predicted three sub-enhancers within the human hs52 enhancer at the FTO locus from the VISTA database, including one missed by existing methods. Using a chicken embryo system and 3D tissue imaging, we showed that each sub-enhancer exhibits restricted spatiotemporal activity within specific subsets of tissues where the full enhancer is active. We further demonstrated VRMOD’s utility for identifying evolutionarily non-conserved enhancers, annotating regulatory sequences in non-model organisms, and identifying candidate disease-causal variants. Collectively, VRMOD provides a universal coordinate reference system for regulatory sequences across 309 vertebrate genomes and enables genome-wide annotation of non-coding regulatory elements in any vertebrate species using genomic sequence alone.

PMID:42745980 | PMC:PMC13575426 | DOI:10.1093/nargab/lqag107