Characterizations of transposable element (TE) landscape in Rhizoctonia solani

Abstract

Rhizoctonia solani is a necrotrophic, basidiomycete fungus which implicates one of the most destructive disease in rice, sheath blight. Here we characterise transposable element (TE) landscape in the assembled genome of R. solani AG1-1A 1802/KB as a prerequisite analysis to further investigate its possible role in pathogenicity and host range. TE characterisation is also subjected to other studied genome of R. solani of different anastomosis groups (AGs) for comparative analysis. In this study, TE is selected as subject due to previous evidences suggesting TE’s influence in driving genome plasticity, host range, pathogenicity and adaptive evolution. First, the genome of R. solani AG1-1A 1802/KB is assembled with only scaffolds which have length of more than 500bp are selected as end product of assembly. Following this, repeat elements covered in the genome are also identified and masked by using a combined approach: both de novo and model-based method. This assembled genome is then subjected to TE identification through TransposonPSI where the same tool was used in all studied R. solani of different AGs. The results obtained are then characterised based on TE classification and superfamily grouping. We reported Class I TE as the most dominant class and Gypsy as the most abundant superfamily, which are consistently observed in all R. solani genome. However, there is slight variation in abundance of TE families reported which may suggest observed differences in host range and infection strategies. This may also be due to the random nature of TE where significant difference in abundance is seen even within the same AG. AG3 which is a dicot-specific pathogen has the lowest TE percentage, and AG1-IA has the highest TE density in the genome. The information derived on the TE landscape and populace within the genomes (distribution, density, families, class) will be used to determine the association to pathogenicity and host range of R. solani..