This study highlights that core and accessory gene families have shaped P. pachyrhizi-soybean interactions, identifying promising targets for functional studies aimed at elucidating host-adaptation mechanisms in rust fungi.
Abstract
Accessory genes are thought to contribute to fungal adaptation and pathogenicity by modulating host immunity, while core genes play crucial roles in maintaining fundamental biological processes. Rust fungi (order Pucciniales) are obligate biotrophic plant-pathogens and infect economically relevant crops. Here, we characterize core and accessory gene repertoires across rust fungi, with a particular focus on Phakopsora pachyrhizi, the causal agent of Asian soybean rust. Across Pucciniales genomes, accessory genes represented the largest fraction of gene content (∼44.6% on average), whereas core genes accounted for a smaller proportion (∼18–35%). Notably, variations in accessory gene content among rust fungi are perhaps attributed to lineage-specific gene expansions and losses. Core gene content was positively correlated with total gene number across Pucciniales genomes, suggesting retention after gene duplication events, consistent with their essential biological functions. Among P. pachyrhizi genes expressed during soybean infection, core effectors were associated with cysteine-rich proteins, pectin-degrading enzymes, and SPFH/Band 7 family, while accessory effectors included phosphatidylethanolamine-binding proteins, trehalose phosphatases, and CFEM domain-containing proteins. The in-plant induced core and accessory genes in P. pachyrhizi also comprised multiple families of CAZymes (GH5/GH7 cellulases, CE5 cutinases, CE8 pectinesterases, CE4/GH18 chitin-modifying enzymes); proteases (aspartyl proteases, serine carboxypeptidases, alpha/beta hydrolases); transporters (amino acid permeases, ferric reductase-like transmembrane proteins, and OPT oligopeptide transporter), and transcription factors (bZIP, GATA zinc finger, STE-like, and homeobox KN). Our study highlights that core and accessory gene families have shaped P. pachyrhizi-soybean interactions, identifying promising targets for functional studies aimed at elucidating host-adaptation mechanisms in rust fungi.
Findings demonstrate that GH28 genes participate in C. pyri infection and identify VP1G_08835 as an important GH28 member required for normal growth and contributing to virulence.
Zi-Yao Xue, Shasha Peng, Zhenzhen Liu et al.· Journal of Fungi· 0 citations
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.
Anand Kumar Shukla, Narendra Y. Kadoo· bioRxiv· 0 citations
Thaumatin-like proteins (TLPs), classified as pathogenesis-related protein 5 (PR-5), constitute an important component of plant defense systems. However, systematic information on the TLP family in sugar beet (Beta vulgaris) remains limited. In this study, a genome-wide investigation of TLP genes was conducted to clarify their genomic features, evolutionary relationships, and expression behavior under biotic stress. A total of 21 TLPs were identified in the sugar beet genome. These genes showed uneven chromosomal distribution and displayed marked variation in gene length, exon-intron organization, and protein physicochemical properties. Phylogenetic analysis of Arabidopsis PR-5 proteins classified the sugar beet members into multiple conserved groups, with consistent gene structure patterns within each group. Expression profiling under Sclerotinia sclerotiorum infection revealed that BvTLP09, BvTLP10, BvTLP12, BvTLP04, and BvTLP01 were strongly induced, whereas other PR-5 genes showed weak, unchanged, or reduced transcriptional responses. Reanalysis of RNA-seq data from beet cyst nematode infection further demonstrated distinct expression patterns between resistant and susceptible varieties at early and late infection stages, indicating dynamic and genotype-dependent regulation of PR-5 genes. This study expands current knowledge of the PR-5 gene family in sugar beet and provides a basis for future functional studies on their roles in pathogen-responsive pathways.
Xuan Duong Vu, Thi Man Le, Thi Ngoc Quynh Le et al.· CTU Journal of Innovation an...· 0 citations
The results suggest that pathogenic variation in Foc is unlikely to be explained by a single conserved virulence determinant or core-genome mutation alone, and contributes a valuable resource for future studies of pepper fusarium wilt.
This study provides new insights into the pangenome of Magnaporthe oryzae and introduces a method for the identification of functionally important genes in fungal species.
Yi Wang, Qi Wu, Jinbin Li et al.· Journal of Advanced Research· 0 citations
The PR10 gene family plays a critical role in plant stress responses. Phylogenetic analysis across species indicated that the PR10 gene first appeared during plant terrestrialization and underwent significant expansion. And, PR10 is conserved in leguminous plants, yet its genomic architecture and functional mechanisms in alfalfa (Medicago sativa L.) remains unclear. In this study, a pan-genomic analysis of 28 alfalfa accessions identified a total of 1657 MsPR10 genes, with tandem duplication accounting for the majority of gene expansion (61.19%). These MsPR10 genes were clustered into 81 Orthologous Gene Groups (OGGs) based on conservative levels, ranging from core to cloud genes. Significant expansion of PR10 genes in Zhongmu No.1 alfalfa (ZMNO) was associated with elevated transposon activity and selective pressure. Transcriptomic analysis indicated MsPR10.SC10 may be a key gene in alfalfa salt-tolerance. Transgenic alfalfa plants overexpressing MsPR10.SC10 were generated by Agrobacterium-mediated transformation. Detailed physiological tests suggested overexpression of MsPR10.SC10 enhanced salt tolerance of alfalfa by maintaining ion homeostasis (reducing Na+/K+ ratio), boosting antioxidant capacity by increasing SOD/ POD activity and reducing H2O2/ MDA accumulation, and regulates the expression of salt stress responsive genes. This study reveals the pan-genomic architecture of the PR10 gene family members in alfalfa, and provides valuable candidate gene for breeding of salt tolerant alfalfa cultivar and may also other crops.