Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB

Abstract

Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungi that damage economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host ranges. The genetic factors driving the unique features of R. solani pathology are not well characterized due to the limited availability of its annotated genomes. Therefore, we performed genome sequencing, assembly, annotation and functional analysis of 12 R. solani isolates covering 7 AGs and select subgroups (AG1-IA; AG1-IB; AG1-IC; AG2-2IIIB; AG3-PT, isolates Rhs 1AP and the hypovirulent Rhs1A1; AG3-TB; AG4-HG-I, isolates Rs23 and R118-11; AG5; AG6; and AG8), in which six genomes are reported for the first time. Using a pangenome comparative analysis of 12 R. solani isolates and 15 other Basidiomycetes, we defined the unique and shared secretomes, CAZymes, and effectors across the AGs. We have also elucidated the R. solani-derived factors potentially involved in determining AG-specific host preference, and the attributes distinguishing them from other Basidiomycetes. Finally, we present the largest repertoire of R. solani genomes and their annotated components as a comprehensive database, viz. RsolaniDB, with tools for large-scale data mining, functional enrichment and sequence analysis not available with other state-of-the-art platforms.

Speciation Underpinned by Unexpected Molecular Diversity in the Mycorrhizal Fungal GenusPisolithus

“…This was first studied within yeasts such as Saccharomyces cerevisiae (63% of orthologs in the core genome of >1k genomes; Peter et al 2018 ), Cryptococcus neoformans , and Candida albicans (80–90% orthogroups form the core genome; McCarthy and Fitzpatrick 2019 ). More recent work with multicellular fungi has found a similar level of genomic conservation ( Zymoseptoria tritici , Badet et al 2020 ; Rhizoctonia solani , Kaushik et al 2020 ; and Neonectria neomacrospora , Nielsen et al 2021 ). Studies that consider a wider diversity of genomes have also found maintenance of a high percentage of gene orthogroups ( Okagaki et al 2016 ; Wang et al 2018 ).…”

Distinct genomic contexts predict gene presence-absence variation in different pathotypes of a fungal plant pathogen

“…Gene PAV plays an important role in fungal pan-genome evolution [2][3][4][5]. To improve our understanding of these events, we designed a robust pipeline to identify orthogroups experiencing PAV in M. oryzae.…”

“…While bacteria typically gain and lose genes in the form of large horizontal gene transfer events [1], the accessory portion of fungal pan-genomes, which is defined in contrast to the conserved set of genes found in all members of a species, are typically shaped by small gene duplication and deletion events, which contribute to gene presence-absence variation (PAV) [2]. Previous fungal pan-genome studies have focused on the roles and functions of core and accessory genes [2][3][4][5], but our knowledge of which genomic and epigenomic features shape fungal pangenomes remains limited. Some studies have highlighted an association of accessory genes with subterminal chromosomal regions and transposable elements (TEs) [2,3], but it is uncertain whether these associations are strong enough to be predictive of gene PAV.…”

Identification and characterization of pathogenicity-related genes of Rhizoctonia solani AG3 during tobacco infection

“…However, relatively few studies have examined the relationship between R. solani AG3 and other economically important crops, including tobacco. Recently, the draft genome sequence of R. solani AG3 became publicly available and was refined, thereby providing thorough knowledge of the architecture, variation, and evolution of the pathogen and enabling more in-depth genetic study of R. solani AG3 ( Shu et al., 2021 ; Kaushik et al., 2022 ).…”