The pangenome analysis of the soil-borne fungal phytopathogen Rhizoctonia solani and development of a comprehensive web resource. Genome sequencing, assembly, annotation and pan-genome analysis of 13 Rhizoctonia solani isolates

Rhizoctonia solani Kühn is a soilborne basidiomycetous fungus that causes significant damage to many economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) with interspecific subgroups having distinctive morphology, pathogenicity and heterogenous genetic composition. However, the genetic factors that drive this diversity, multi-host preference and unique fungal pathology are still unclear due to the limited number of available genomes sequences and the gene models. Therefore, we performed genome sequencing, assembly, annotation and pangenome functional analysis of 13 R. solani isolates covering 7 AGs and selected subgroups (AG1-IA, AG1-IB, AG1-IC, AG2-2IIIB, AG3-PT, AG3-TB, AG4-HG-I, AG5, AG6, and AG8). The comparative analysis reveals high similarities among different AGs along with unique attributes associated with each isolate. We predicted a range of pathogenic processes in different subgroups and genetic factors potentially involved in determining AG-specific host preference. Finally, we present the largest repertoire of reference-quality R. solani genomes and their annotated gene models, compiled as a comprehensive and user-friendly database, viz. RsolaniDB. Since 7 genomes are reported for the first time, the database stands as a valuable platform for formulating new hypotheses by hosting R solani genome assemblies and gene models, with tools for functional enrichment, orthologs and sequence analysis.