Author: slquinlan

BMC Genomics. 2026 Jan 15. doi: 10.1186/s12864-025-12493-x. Online ahead of print.

ABSTRACT

BACKGROUND: The soybean cyst nematode (SCN) is a persistent threat to soybean production. SCN populations continually overcome resistant cultivars, causing significant yield losses. Studies conducted with a single reference genome restrict our understanding of intraspecific diversity, masking significant mechanisms of virulence evolution and host adaptation. Here we report a pangenome constructed of nine SCN populations of different pathotypes, including eight newly generated high-fidelity genome assemblies.

RESULTS: We detected over 19,000 orthologous gene families and more than 12,000 putative secreted proteins in SCN. Combined, these data indicate substantial diversity across populations. Gene content analysis showed that 35% of gene families were the conserved core, 15% were soft-core, and 48% were accessory. Evidence of rapid evolution was identified in a high portion (40%) of core single-copy genes, most notably inside the protein domains responsible for host recognition and immune modulation. Analysis of gene-family expansion revealed extensive duplication and loss across lineages, suggesting ongoing paralog turnover within SCN populations. Finally, a graph-based pangenome enabled the identification of numerous structural variants within regions under selection.

CONCLUSIONS: Our study highlights substantial genetic variation in SCN that is not captured by single-reference analyses. By integrating multiple high-quality assemblies, we show that the SCN genome is highly dynamic, with extensive gene duplication and loss as well as structural variation shaping the differences among nematode populations. Collectively, the SCN pangenome provides a robust resource for studying virulence and adaptation mechanisms in SCN and establishes a genomic foundation for the development of more precise management strategies.

PMID:41535767 | DOI:10.1186/s12864-025-12493-x

Phytopathology. 2026 Jan 8. doi: 10.1094/PHYTO-08-25-0283-R. Online ahead of print.

ABSTRACT

Infection by aphid-transmitted poleroviruses modulates gene expression associated with plant development and defense. This study assessed the gene expression patterns following cotton leafroll dwarf virus (CLRDV) infection in primary and alternate hosts. Two comparisons (CLRDV-infected vs. non-infested and mock-inoculated vs. non-infested) were evaluated to identify differentially expressed genes (DEGs), and to tease out differences in gene expression profiles between aphid feeding and aphid-mediated CLRDV infection in each host. CLRDV infection was characterized by 2079, 1238, 1484, and 1773 DEGs in the primary host cotton, and in alternate hosts hibiscus, okra, and prickly sida, respectively. The number of DEGs upon aphid feeding was less than CLRDV infection in all hosts except okra. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms identified DEGs associated with development, defense, and vector fitness influencing compounds (VFICs) in CLRDV-infected plants. Genes associated with phytohormones, photosynthesis, salicylic acid, jasmonic acid, pathogenesis related proteins, heat shock proteins, transcription factors, membrane transporters, terpenoids, carbohydrates, and amino acids were differentially expressed in CLRDV-infected plants and varied between hosts. Few overlapping and numerous unique genes in the above-stated categories were differentially expressed upon aphid feeding and varied between hosts. DEGs associated with signaling pathways, transcription factors, systemic resistance, pathogenesis related proteins, and carbohydrate and amino acid biosynthesis were common between aphid-mediated CLRDV infection and aphid feeding alone. The observed gene expression patterns reiterate that differences in host susceptibility to the virus and/or the vector could differentially influence host defense and development, and vector fitness.

PMID:41504669 | DOI:10.1094/PHYTO-08-25-0283-R

bioRxiv [Preprint]. 2025 Dec 17:2025.12.17.694939. doi: 10.64898/2025.12.17.694939.

ABSTRACT

Pattern-triggered immunity (PTI) provides broad-spectrum protection in plants by activating defense responses upon perception of conserved microbial signatures such as bacterial flagellin. In vitro transcriptome profiling revealed that the Pseudomonas syringae pv. tomato DC3000 two-component regulator CvsR mirrors some of the broader regulatory patterns observed under the exposure to PTI in planta. Our analyses indicated that during infection in planta, CvsR primarily governs a small core regulon centered on carbonic anhydrase and its associated transporter. Comparative RNA-seq analyses between the ΔcvsR and wild type strain further confirm this narrow regulatory scope. Moreover, the majority of bacterial transcriptional shifts appear to reflect indirect consequences of response to the host immune environment rather than direct CvsR-dependent regulation, including responses associated with sulfate starvation. Together, these findings suggest that PTI-driven bacterial transcriptional reprogramming is shaped predominantly by host immune status, with CvsR exerting modest, targeted control restricted to a limited set of genes.

PMID:41446199 | PMC:PMC12724701 | DOI:10.64898/2025.12.17.694939

G3 (Bethesda). 2026 Jan 3:jkaf317. doi: 10.1093/g3journal/jkaf317. Online ahead of print.

ABSTRACT

Yellow wood sorrel (Oxalis stricta L.), also known as sourgrass, juicy fruit, or sheep weed, is a member of the Oxalidaceae family. Yellow wood sorrel is commonly considered a weed and while native to North America, it is distributed across Europe, Asia, and Africa. To date, only two other genomes from the Oxalidaceae family have been published, star fruit (Averrhoa carambola L.) and Oxalis articulata Savingy. Here, we present a chromosome-scale assembly for O. stricta, revealing its allotetraploid nature and synteny within its two subgenomes as well as synteny with A. carambola and O. articulata. Using Oxford Nanopore Technologies long-read sequences coupled with chromatin capture sequencing, we generated a 436 Mb chromosome-scale assembly of O. stricta with a scaffold N50 length of 36.2 Mb that is anchored to 12 chromosomes across the two subgenomes. Assessment of the final genome assembly using the Long Terminal Repeat Assembly Index yielded a score of 13.12 and assessment of Benchmarking Universal Single Copy Orthologs revealed 99.6% complete orthologs; both metrics are suggestive of a high-quality reference genome. Total repetitive sequence content in the O. stricta genome was 39.7% with retroelements being the largest class of transposable elements. Annotation of protein-coding genes yielded 61,550 high confidence genes encoding 115,089 gene models. Synteny between the two O. stricta subgenomes was present in 93 syntenic blocks containing 40,750 genes, of which, 76.47% were present in 1:1 syntenic relationships between the two subgenomes. The availability of an annotated chromosome-scale high quality genome assembly for O. stricta will provide a launching point to understand the high fecundity of this weed and provide further foundation for comparative genomics within the Oxalidaceae.

PMID:41482730 | DOI:10.1093/g3journal/jkaf317

J Comput Chem. 2026 Jan 5;47(1):e70298. doi: 10.1002/jcc.70298.

ABSTRACT

Pectin, a major class of matrix polysaccharides present in plant cell walls (PCW), contains widespread anionic saccharides that cross-link in the presence of cations. It modulates important functions such as cell-cell adhesion and determines the PCW’s biomechanical properties. It is known that mono-, di-, and tri-valent cations facilitate cross-linking; however, significant knowledge gaps remain in understanding the structure and mechanism of pectin cross-linking. In this study, replica-exchange molecular dynamics (REMD) simulations were employed to elucidate the role of ionic charge, ionic radii, and functional groups on the cross-linking of homogalacturonan (HG), the most abundant pectin molecule. Our enhanced sampling approach in fully solvated environments suggests more effective cross-linking with higher-valent and smaller ions, and that the “zipper” conformation is more favorable than the prevalent “egg-box” conformation. These findings advance our fundamental understanding of pectin matrix structure in PCWs and provide a solid foundation to probe structure-property relationships in pectic polysaccharides.

PMID:41472421 | DOI:10.1002/jcc.70298

Plants (Basel). 2025 Dec 18;14(24):3860. doi: 10.3390/plants14243860.

ABSTRACT

Cold stress limits cucumber productivity, and grafting onto tolerant rootstocks offers a promising strategy for improving resilience. This study compared the responses of cucumber heterografts and self-grafts exposed to different cold temperatures, aiming to uncover the molecular basis of grafting-mediated tolerance. Morphological observations showed that grafting onto Cucurbita ficifolia and C. maxima X C. moschata cv. Tetsukabuto rootstocks improved plant growth under moderate cold, while extreme stress remained lethal. Transcriptome analysis revealed that heterografts displayed broader and more sustained differentially expressed genes than self-grafts. Gene ontology (GO) enrichment in heterografts indicated early activation of structural, regulatory, and metabolic processes, with continued enrichment at later stages. KEGG analysis highlighted plant hormone signaling as a central pathway modulated by heterografting, with selective regulation of auxin, ethylene, and ABA signaling. Heterografts activated key regulators, including MAPK3-like, TIFY5A, and CPK28, which were strongly expressed, alongside transcription factors from NAC, CAMTA, WRKY, and MYB families, suggesting coordinated regulation of cold-responsive networks. These results demonstrate that heterografting enhances cold tolerance by orchestrating multi-layered molecular responses, including hormone modulation, stress signaling, and transcriptional factors. This underscores the potential of grafting onto cold-tolerant rootstocks as a practical strategy for cucumber cultivation in cold-prone environments.

PMID:41470743 | PMC:PMC12736856 | DOI:10.3390/plants14243860

Toxins (Basel). 2025 Dec 15;17(12):596. doi: 10.3390/toxins17120596.

ABSTRACT

The year 2025 marks two significant milestones for aflatoxin research: 65 years since aflatoxin was first identified in 1960, and 50 years of focused research on preharvest aflatoxin contamination since it was first recognized in 1975. Studies in the 1970s revealed that A. flavus could infect crops like maize and produce aflatoxin in the field before harvest and made it possible to investigate the potential genetic resistance in crops to mitigate the issues. Tremendous efforts have been made to learn about the process and regulation of aflatoxin production along with interactions between A. flavus and host plants as influenced by environmental factors. This has allowed for the breeding of more resistant crops and investigations into the underlying genetic and genomic components of resistance mechanisms in crops like maize and peanut. However, despite decades of studies, many questions remain. One established “dogma” is that drought stress, especially when combined with high temperatures, is the single greatest contributing factor to preharvest aflatoxin contamination and is a perennial risk faced throughout the major agricultural production regions of the world. Although there are many reviews summarizing the decades’ long wealth of information about A. flavus, aflatoxin biosynthesis, management and host plant resistance, there are few reports that put the spotlight on why aflatoxin contamination is exacerbated by drought stress, which places plants under severe physiological stress and weakens immune systems. Therefore, here we will focus on three major areas of research in maize: the “living embryo” theory and host resistance mechanisms, the “Key Largo hypothesis” and the causes of drought-exacerbated aflatoxin contamination, and recent advancements in CRISPR-based genome editing for enhancing drought tolerance and increasing plant immune responses. This will highlight key breakthroughs and future prospects for the continuing development of superior crop germplasm and cultivars and for mitigating aflatoxin contamination in food and feed supply chains.

PMID:41441631 | DOI:10.3390/toxins17120596

Plant J. 2025 Dec;124(6):e70617. doi: 10.1111/tpj.70617.

ABSTRACT

This study, the third in a three-part series, investigates whether chromosomal instability persists in cultivated peanut. The allotetraploid peanut (Arachis hypogaea; genome type AABB) originated from the hybridization and polyploidization of A. duranensis (AA) and A. ipaënsis (BB). Our first study established that this was an extremely narrow genetic origin, likely from a single hybridization event. This raised a paradox: how did such narrow genetics give rise to the phenotypic diversity seen in cultivated peanut? The second study addressed this, showing that a single neoallotetraploid spontaneously generates striking diversity, and that homoeologous exchanges-abundant in early generations following polyploidy-are a key mechanism in creating this diversity. In contrast to this early-generation instability, cultivated peanut is generally considered to be genetically stable, presumably due to selection. This third study tests whether residual instability still occurs in modern peanut. From a single plant of the highly selfed ‘genome stock’ of the cultivar ‘Tifrunner’, we advanced lineages through seven generations in a pollinator-free greenhouse. Among 233 plants, we identified three new large-scale chromosomal instability events: a large deletion on chromosome B01, associated with reduced pod width and seed weight, and two ABBB compositions involving chromosomes A02/B02 and A05/B05. With these observations in hand, we reinterpreted previously published data from two recombinant inbred populations. Together, these results indicate that at least 1% of pure pedigree A. hypogaea plants exhibit spontaneous large-scale chromosomal changes-a surprising frequency of instability that likely contributes to peanut’s long-term adaptability and evolution.

PMID:41443178 | DOI:10.1111/tpj.70617

Plant J. 2025 Dec;124(6):e70618. doi: 10.1111/tpj.70618.

ABSTRACT

This study, the second in a three-part series, shows how peanut’s polyploid origin enabled rapid diversification and enhanced domestication potential. Building on the knowledge that cultivated peanut (Arachis hypogaea) originated from a narrow hybridization between Arachis duranensis and Arachis ipaënsis less than 10 000 years ago, we are confronted with a paradox: how did such a narrow origin give rise to so much diversity-two subspecies, six botanical varieties, and thousands of landraces differing in growth habit, seed size, and pod morphology? Although several diploid Arachis species were cultivated earlier, only the allotetraploid became fully domesticated and widely adopted. The global success of peanut, despite its narrow genetic origin, suggests that polyploidization itself facilitated domestication. To test this hypothesis, we investigated how the two diploid progenitors and neoallotetraploids derived from a single hybridization and polyploidization event responded under artificial selection. In a pollinator-free greenhouse, we advanced lineages of the neoallotetraploid and its diploid parents over 6 years, selecting for divergent seed weights. The neoallotetraploid showed a much stronger response to artificial selection than its diploid parents, while also spontaneously generating diverse phenotypic variation-including flower color, pod reticulation, and chlorophyll content-traits that distinguish A. hypogaea subspecies and landraces. These traits mirrored directional shifts in parental genome dosage caused by homoeologous exchange, supporting a causal connection with phenotype. These findings offer a compelling rationale for a domestication advantage in polyploid peanut, and provide a living demonstration of how a single ancestral tetraploid, despite an extreme genetic bottleneck, generates a phenotypic boom.

PMID:41443173 | DOI:10.1111/tpj.70618

Plant J. 2025 Dec;124(6):e70619. doi: 10.1111/tpj.70619.

ABSTRACT

This study, the first in a three-part series, lays the foundation for understanding the origin of the peanut crop (Arachis hypogaea). Its subsequent evolution is explored in the two papers that follow. The evidence that A. hypogaea originated from a single hybridization event between Arachis duranensis and Arachis ipaënsis less than 10 000 years ago was already very strong. Here, we extend this evidence using more than 1600 single-nucleotide polymorphisms to make an almost exhaustive comparison of wild Arachis section germplasm conserved ex situ with the A and B subgenomes of divergent, sequenced cultivated peanuts. The wild relatives of peanut are highly selfing and their geocarpy means they plant their own seeds, allowing them to persist as discrete populations for millennia. This unusual biology creates a rare opportunity for genetic archaeology: ancestral lineages can be identified with exceptional precision. Our results reaffirm a single origin for the cultigen, identifying A. duranensis from Río Seco and A. ipaënsis K 30076 as the closest known relatives of the A and B subgenomes of peanut. As a genomic resource, we generated a chromosome-scale assembly of the Río Seco A. duranensis K 30065 and confirmed that it is more closely related to the A subgenome of peanut than the current reference genome (V14167). Even if somewhat closer wild accessions were found through new field collections, they would still belong to the same ancestral lineage. With this level of evidence, the origin of peanut is now known in greater detail than that of any other ancient polyploid crop.

PMID:41442708 | DOI:10.1111/tpj.70619