Host-driven structuring shapes the landscape of phytoplasma diversity across Indian agroecosystems revealed by multilocus phylogenomics

Mitochondrial genomic variation, evolutionary dynamics, and phylogeny of forest-associated Phytophthora species in the Qinling Mountains of China

Combined mitogenomic and multi-locus phylogenomics clarified the phylogenetic placement of these taxa and provided timescale estimates for their divergence and enriches the mitogenomic resources of Phytophthora from pristine natural ecosystems.

High Genotypic Polymorphism and Extensive Gene Flow Drive the Population Dynamics of Potato Oomycete Pathogen, Phytophthora infestans, Across Southwestern China

Potato late blight, Phytophthora infestans, remains a major global threat to potato production due to the rapid genetic change, long-distance dispersal and fungicide resistance. To clarify the genetic structure and phenotypic characteristics of P. infestans populations in southwestern China during 2019–2025, this study analyzed 241 isolates collected from Sichuan, Chongqing, Guizhou, Yunnan and Hubei. The isolates were characterized using 14 SSR markers, together with mating-type determination, metalaxyl sensitivity assays, mitochondrial haplotype identification and virulence profiling. A total of 70 alleles and 118 multilocus genotypes were detected, with certain genotypes (SW-40, SW-48 and SW-81) broadly distributed across regions, while the simultaneous presence of numerous low-frequency genotypes reflected high overall genetic diversity. Population genetic analyses revealed weak regional differentiation and strong genetic connectivity, with most genetic variation occurring within regional populations, where self-fertile isolates, metalaxyl-resistant phenotypes and mitochondrial haplotype Ia were predominant. Cluster and principal component analyses separated the isolates into three major genetic groups, with the largest group containing most isolates and showing close genetic similarity to the Blue_13 reference genotype. These findings indicate that southwestern China harbors a highly diverse and admixed P. infestans population, likely driven by frequent pathogen movement among potato-growing regions.

Global‐Scale Patterns of Host Transitions Suggest Contrasting Levels of Specialization Within Rhizoctonia solani

ABSTRACT The ability of plant pathogens to infect multiple host species has substantial adverse effects on food security and ecosystem health. Rhizoctonia solani is a globally distributed, soil‐borne fungal pathogen capable of infecting a wide variety of economically important crops. Its broad distribution across geographic regions and host taxa is accompanied by high genetic diversity. Historically, the R. solani species complex has been classified into 14 anastomosis groups (AGs) based primarily on hyphal anastomosis compatibility. Despite being widely perceived as a generalist, R. solani's host range has not been studied in a comprehensive cross‐AG framework to evaluate global patterns of pathogen diversity and host associations. We analyzed a global dataset of 4119 R. solani rDNA‐ITS sequences collected over the past 70 years, including newly sampled taxa from Nebraska, and used a smaller concatenated ITS and TEF‐1α dataset comprising 162 R. solani sequences to assess whether broad phylogenetic patterns were consistent across markers. Phylogenetic reconstruction suggests that most AGs formed well‐supported clades that largely corresponded to reported AG designations. Host family‐level transition inference suggests that generalist AGs may experience more transient host associations, while specialist lineages show stronger host‐associated genetic differentiation that contributes to the observed genetic structure. Our ancestral host‐state reconstruction analysis further suggests that the AG‐3 lineage likely originated from an ancestor with a broader host range and subsequently became predominantly associated with Solanaceae, with no inferred reversal in the sampled dataset. These findings suggest that host association and host‐transition patterns are important features of the generalism‐specialization continuum and contribute to population structure in a globally distributed fungal pathogen.

Integrated Pangenomic and Systems Biology Analyses Reveal the Genomic Basis of Virulence and Adaptation in Bipolaris sorokiniana

The first comprehensive species-wide pangenomic and systems-level analyses of B. sorokiniana are presented, providing vital insights into the evolutionary architecture of pathogenicity, adaptation, and genome diversification and providing a valuable genomic resource for disease surveillance and functional characterization of virulence determinants.

Evaluation of genetic diversity among Kosovo maize landraces by retrotransposon-based IRAP marker

Nuclear genome population genomics of the potato wart pathogen (Synchytrium endobioticum) reveals high-resolution relationships of global strains

A robust single-nucleotide polymorphism (SNP) discovery strategy is designed and applied to existing and novel sequence data sets that represent the global diversity in potato production systems and indicates that potato wart was introduced into Canada from a European source.