Author: slquinlan

Phytopathology. 2026 Feb 13. doi: 10.1094/PHYTO-10-25-0349-R. Online ahead of print.

ABSTRACT

Understanding how biotic and abiotic factors influence vector-borne pathogen spread is essential for effective management. Cotton leafroll dwarf virus (CLRDV), transmitted by the cotton aphid, Aphis gossypii Glover, can cause yield loss in cotton, Gossypium hirsutum L. CLRDV has a variable incidence across the Cotton Belt, but factors underlying this variation are unknown. Field surveys of commercial cotton fields conducted in Alabama and Georgia from 2021-2022, allowed collection of data on A. gossypii, natural enemies, CLRDV weed hosts, CLRDV incidence, landscape composition, temperature, and precipitation. A structural causal modeling analysis using a directed acyclic graph framework was used to test the significance of these factors on CLRDV incidence in cotton while controlling for potentially confounding effects. Aphis gossypii abundance, prevalence of cotton in the landscape, and temperature had significant and positive effects on CLRDV incidence, whereas other variables were not significant. Temperature had a significant and positive effect on A. gossypii abundance, which likely contributed to the overall effect of temperature on CLRDV incidence. Cotton is a host for both the vector and virus, which may increase the abundance of both. Novel findings from this study identify factors associated with regions at high-risk for CLRDV. Future work can leverage these findings to better predict the spatial and temporal variability in disease incidence.

PMID:41687252 | DOI:10.1094/PHYTO-10-25-0349-R

Bio Protoc. 2026 Feb 5;16(3):e5579. doi: 10.21769/BioProtoc.5579. eCollection 2026 Feb 5.

ABSTRACT

The plant cell wall is a dynamic and complex extracellular matrix that not only provides structural integrity and determines cell shape but also mediates intercellular communication. Among its major components, pectins play essential roles in cell adhesion, wall porosity, hydration, and flexibility. Rhamnogalacturonan-I (RG-I), a structurally diverse pectic polysaccharide, remains one of the least understood components of the plant cell wall. Its backbone is substituted with arabinan, galactan, and arabinogalactan side chains that vary in length, branching, and composition across tissues, species, and developmental stages. In addition, RG-I can undergo modifications such as backbone acetylation, further contributing to its structural complexity and functional diversity. To advance understanding of RG-I, we present a detailed method for isolating RG-I from the model plant Arabidopsis thaliana. Leveraging Arabidopsis as a model system provides major advantages owing to its well-characterized genome and powerful molecular toolkit, enabling deeper investigation into the roles of RG-I in plant development and responses to environmental stress. Our method consists of two major steps: an initial chemical extraction using oxalate, followed by endo-polygalacturonase (EPG) digestion to fragment the pectic domains. An advantage of this approach is that it produces a dry material that can be stored at room temperature without special handling and does not introduce chemicals that may interfere with downstream analyses. The purified RG-I can be used for detailed compositional and structural analyses, as well as for functional studies of enzymes involved in pectin biosynthesis, modification, and degradation. Although this protocol was developed for isolating RG-I from Arabidopsis rosette leaves, it is also applicable to other Arabidopsis organs and other plant species. Key features • This protocol provides a detailed description of RG-I isolation from Arabidopsis rosette leaves. • The isolated RG-I can be used for compositional and structural analyses and serves as a substrate for functional studies of enzymes. • This protocol is also applicable for isolating RG-I from other Arabidopsis organs and from different plant species.

PMID:41675992 | PMC:PMC12887878 | DOI:10.21769/BioProtoc.5579

Microb Genom. 2026 Feb;12(2). doi: 10.1099/mgen.0.001624.

ABSTRACT

Pantoea allii, one of four Pantoea species known to cause onion centre rot, is infrequently isolated from onion compared to its closely related onion-pathogenic species in the same genus. To better understand the genomic diversity and genetic determinants of pathogenicity in this species, we analysed a collection of 38 P. allii strains isolated from 2 primary ecological niches, plants and rainwater, across North and South American and African continents using comparative genomics and phylogenetic approaches. Core-genome phylogeny, average nucleotide identity and gene presence-absence analyses revealed three genetically distinct lineages. All strains harboured conserved biosynthetic gene clusters (BGCs) for quorum sensing, carotenoid production, siderophores and thiopeptides. In contrast, two phosphonate BGCs, key determinants of onion pathogenicity, exhibited lineage-specific distributions. Onion-associated strains from lineages 1 and 2 carried the Halophos BGC responsible for onion tissue necrosis and also encoded the alt gene cluster that confers tolerance to thiosulfinates. Lineage 3 strains, isolated from both onion and rainwater, either lacked a phosphonate BGC entirely or possessed the HiVir phosphonate BGC. In addition, lineage 3 strains lacked the alt cluster altogether. The localization of these virulence genes in the genome varied, with Halophos integrated in the chromosome, HiVir encoded on the conserved Large Pantoea Plasmid, and alt located on small, variable plasmids (plasmid B). The type IV secretion system (T4SS) and type VI secretion system (T6SS) showed variable genomic architectures, with plasmid-borne T4SSs and two chromosomal T6SS loci differing in conservation and gene content. Additionally, conserved Pantailocin phage islands were detected in most genomes. Overall, this study reveals that while core metabolic and competitive traits are conserved across P. allii, virulence-associated loci display lineage-specific distribution, reflecting ecological differentiation and evolutionary plasticity within the species.

PMID:41637125 | DOI:10.1099/mgen.0.001624

Proc Natl Acad Sci U S A. 2026 Feb 10;123(6):e2520476123. doi: 10.1073/pnas.2520476123. Epub 2026 Feb 3.

ABSTRACT

Proteins secreted from a mouth stylet of sedentary plant-parasitic root-knot nematodes self-polymerize to form a unique feeding tube structure within host cells modified into giant feeding cells by the nematode. Feeding tubes have essential functions as they complex with the host endomembrane system for nutrient uptake to sustain parasitism. Despite their significance, they remain one of the least understood aspects of nematode parasitism of plants. Their small size and location within giant-cells deeply embedded within galls encasing adult females has prohibited studies to isolate and discern their molecular composition. Here, we developed a protocol for the isolation and semipurification of root-knot nematode feeding tubes from giant-cell cytoplasm of several host plant species to provide a unique view of these structures at the light and scanning electron microscopy level revealing previously undescribed features of their structure. Our methods allowed for the isolation and solubilization of sufficient quantities of enriched feeding tubes enabling a comparative proteome analysis across host species that identified proteins with an increased likelihood to function in feeding tube formation. A comparison across root-knot nematode species further narrowed candidates to a conserved class of secretory proteins that specifically localized within secretory granules of the dorsal gland of adult females and in feeding tubes formed within host cell cytoplasm to unequivocally demonstrate these proteins as core components of feeding tubes. Our finding gives scientists a look into the protein composition of feeding tubes opening the door to a better understanding of their structure and function in nematode parasitism.

PMID:41632840 | DOI:10.1073/pnas.2520476123

G3 (Bethesda). 2026 Jan 30:jkag021. doi: 10.1093/g3journal/jkag021. Online ahead of print.

ABSTRACT

Genome sequence contamination has a variety of causes and can originate from within or between species. Previous research focused on contamination between distantly related species or on prokaryotes. Here we test for intra-species contamination by mapping short read genome data to a reference and visualizing the frequency of reads with single nucleotide di_erences from the reference. Out of 1,298 publicly available genome sequences investigated for Saccharomyces cerevisiae, a small number (8 genomes) show at least 5% contamination. Contamination rates di_ered however among sequencing centers: one unusually large study had a low contamination rate (below 0.2%) but the contamination rate was higher for other studies (2% or 15% of genomes). Using genome data contaminated in silico to known degrees, we showed that contamination is recognizable in plots with unexpected secondary allele (B-allele) frequencies of at least 5% and measured contamination e_ects on admixture and phylogenetic analysis in two fungal species. With a standard base calling pipeline, we found that contaminated genomes super_cially appeared to produce good quality genome data. Yet as little as 5-10% genome contamination was enough to change phylogenetic tree topologies and make contaminated strains appear as hybrids between lineages (genetically admixed). We recommend the use of B-allele frequency plots to screen genome resequencing data for intra-species contamination.

PMID:41616078 | DOI:10.1093/g3journal/jkag021

Mol Biol Evol. 2026 Jan 23:msag020. doi: 10.1093/molbev/msag020. Online ahead of print.

ABSTRACT

Meiotic drivers are selfish genetic elements that gain transmission advantages by distorting equal, Mendelian segregation. For decades, biologists have considered meiotic drivers as interesting, albeit esoteric, case studies. It is now clear, however, that meiotic drive is more common and phylogenetically widespread than previously supposed. Indeed, intensive study of a few well-known cases has begun to reveal the evolutionary genomic consequences of meiotic drive. We argue here that many features of genome evolution, content, and organization that are seemingly inexplicable by organismal adaptation or nearly neutral processes are instead best accounted for by recurrent histories of meiotic drive. We review how meiotic drive can affect the evolution of sequences, gene copy numbers, genes with functions in meiosis and gametogenesis, signatures of “selection”, chromosome rearrangements, and karyotype evolution. We also explore the interactions of meiotic drive elements with other classes of selfish genetic elements, including satellite DNAs, transposable elements, and with the endogenous host genes involved in drive suppression. Finally, we argue that some aspects of drive-mediated genome evolution are now sufficiently well established that we might reverse the direction of discovery- rather than ask how drive affects genome evolution, we can use genome data to discover new putative drive elements.

PMID:41589062 | DOI:10.1093/molbev/msag020

Int J Syst Evol Microbiol. 2026 Jan;76(1). doi: 10.1099/ijsem.0.007043.

ABSTRACT

Three bacterial strains, AG2a^T, AX9b^T and BK9b, were isolated from symptomatic onion bulbs (Allium cepa) collected in the USA between 2013 and 2016. Phylogenomic analyses based on whole-genome sequencing, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) revealed that strain AG2a^T belongs to a novel species within the genus Phytobacter, and strains AX9b^T and BK9b represent a novel species within the genus Kosakonia. ANI and isDDH values between these strains and their closest relatives were well below the species delineation thresholds (ANI <85.3%, isDDH <27.9%), and they were phenotypically different from their closest phylogenomic neighbours. Genomic assemblies yielded complete circular chromosomes and plasmids, with G+C contents ranging from 53.48% to 53.70%. Despite nitrogen fixation being a characteristic trait of both genera, none of the strains harboured the nif operon. Based on these results, we propose the establishment of the two novel species Phytobacter cepae sp. nov., with strain AG2a^T as the designated type strain (= CCOS 2093^T = CFBP 9466^T) and Kosakonia beeri sp. nov., with strain AX9b^T as the designated type strain (= CCOS 2091^T = CFBP 9467^T).

PMID:41587076 | DOI:10.1099/ijsem.0.007043

Mol Biol Evol. 2026 Jan 25:msag003. doi: 10.1093/molbev/msag003. Online ahead of print.

ABSTRACT

The relatively young and repeated evolutionary origins of dioecy (separate sexes) in flowering plants enable investigation of molecular dynamics occurring at the earliest stages of sex chromosome evolution. With two independently young origins of dioecy, Asparagus is a model genus for studying the genetics of sex-determination and sex chromosome evolution. Dioecy first evolved in Asparagus ∼3-4 million years ago (Ma) in the ancestor of a now widespread Eurasian clade including garden asparagus (Asparagus officinalis). A second origin occurred in a smaller, geographically restricted, Mediterranean Basin clade including Asparagus horridus. New haplotype-resolved reference genomes for garden asparagus and A. horridus, elucidate contrasting first steps in the origin of the sex chromosomes of the Eurasian and Mediterranean Basin clade ancestors. Analysis of the A. horridus genome revealed an XY system derived from different ancestral autosomes with different sex-determining genes than have been characterized for garden asparagus. We estimate that proto-XY chromosomes evolved 1-2 Ma in the Mediterranean Basin clade, following an ∼2.1-megabase inversion that now distinguishes the X and Y chromosomes. Recombination suppression and LTR retrotransposon accumulation drove the expansion of the male-specific region on the Y (MSY) that reaches ∼9.6-megabases in A. horridus. The garden asparagus genome revealed an MSY spanning ∼1.9-megabases. A segmental duplication and neofunctionalization of one duplicated gene (SOFF) drove the origin of dioecy in the Eurasian clade. These findings support previous inference based on phylogeographic analysis revealing two recent origins of dioecy in Asparagus and establish the genus as a model for investigating sex chromosome evolution.

PMID:41581085 | DOI:10.1093/molbev/msag003

Plant Genome. 2026 Mar;19(1):e70169. doi: 10.1002/tpg2.70169.

ABSTRACT

Commercial potato (Solanum tuberosum) in North America is a clonal autotetraploid crop, which complicates breeding. Efforts are underway to convert potato to a diploid inbred-hybrid crop, allowing breeders to more quickly meet market and environmental demands. With the goal of preserving haplotypes developed over 200 years of selection, diploid potato breeding in the United States started with the creation of diploids from tetraploid commercial varieties and advanced breeding lines through prickle pollination. This is an effective but slow method, which presents a barrier to entry for individual breeding programs. Therefore, we developed 97 publicly available dihaploids (diploids from prickle pollination of tetraploids) as a resource for diploid breeding in the United States. These clones contain the majority of alleles in the US breeding population for three market classes: chips, russets, and fresh market reds. To facilitate genomic informed breeding, all clones have been resequenced, and we have developed de novo assemblies for 20 individuals. As an illustration of how these data will be used in breeding, we explored the maturity locus (StCDF1) and identified 15 different alleles. The majority of dihaploids were heterozygous for early and late alleles, resulting in intermediate maturity. Beyond informing breeding, these data facilitate investigations into potato genomics. The dihaploid population is both highly heterozygous and incredibly diverse on a population level. In particular, there is extensive structural diversity segregating within the population. This contrasts with a relatively low genome-wide historical recombination rate (ρ), indicating that much of potato’s high diversity is found within long linkage blocks.

PMID:41543114 | DOI:10.1002/tpg2.70169

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