The pangenome analysis of the soil-borne fungal phytopathogen Rhizoctonia solani and development of a comprehensive web resource: RsolaniDB

Authors: KAUSHIK, ABHINAV - King Abdullah University Of Science And Technology; Roberts, Daniel; RAMAPRASAD, A - King Abdullah University Of Science And Technology; MFARREJ, S - King Abdullah University Of Science And Technology; NAIR, M - King Abdullah University Of Science And Technology; Lakshman, Dilip; PAIN, ARNAB - King Abdullah University Of Science And Technology

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/8/2022
Publication Date: 3/25/2022
Citation: Kaushik, A., Roberts, D.P., Ramaprasad, A., Mfarrej, S., Nair, M., Lakshman, D.K., Pain, A. 2022. The pangenome analysis of the soil-borne fungal phytopathogen Rhizoctonia solani and development of a comprehensive web resource: RsolaniDB. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2022.839524.
DOI: https://doi.org/10.3389/fmicb.2022.839524

Interpretive Summary: Rhizoctonia solani Kühn is a complex of soilborne plant pathogenic fungi that cause significant economic damage to many agriculturally important crops. Identification and differentiation of the many similar appearing R. solani species within this pathogen complex is necessary as individual species vary in response to plant disease control measures. Genomes of 13 isolates from the Rhizoctonia solani plant pathogen complex were sequenced, assembled, and annotated – and a genome database created (http://rsolanidb.kaust.edu.sa /RhDB/). This database provides information to scientists that is critical for development of identification methods for different isolates within the R. solani pathogen complex. Once these identification methods are developed, the correct disease control measures can be applied to decrease economic loss caused by this pathogen complex. This information will be useful to scientists developing identification measures for fungal species within this species complex, as well as to scientists determining the molecular basis of disease caused by these important plant pathogens.

Technical Abstract: 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 functionally annotated genomes. 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 revealed unique attributes associated with each isolate along with similarities among different AGs. We predicted a range of pathogenic attributes 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.