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Background  Sugar beet ( Beta vulgaris ) is a crop cultivated for its high content in sugar, but it is vulnerable to many soil-borne pathogens. One of them is the basidiomycete  Rhizoctonia solani . This fungal species has a compatibility system regulating hyphal fusions (anastomosis). Consequently,  R. solani  species are categorized in anastomosis groups (AGs). AG2-2IIIB isolates are most aggressive on sugar beet. In the present study, we report on the draft genome of  R. solani  AG2-2IIIB using the Illumina technology. Genome analysis, interpretation and comparative genomics of five sequenced  R. solani  isolates were carried out.    Results  The draft genome of  R. solani  AG2-2IIIB has an estimated size of 56.02 Mb. In addition, two normalized EST libraries were sequenced. In total 20,790 of 21,980 AG2-2IIIB isotigs (transcript isoforms) were mapped on the genome with more than 95 % sequence identity. The genome of  R. solani  AG2-2IIIB was predicted to harbor 11,897 genes and 4908 were found to be isolate-specific.  R. solani  AG2-2IIIB was predicted to contain 1142 putatively secreted proteins and 473 of them were found to be unique for this isolate. The  R. solani  AG2-2IIIB genome encodes a high number of carbohydrate active enzymes. The highest numbers were observed for the polysaccharide lyases family 1 (PL-1), glycoside hydrolase family 43 (GH-43) and carbohydrate estarase family 12 (CE-12). Transcription analysis of selected genes representing different enzyme clades revealed a mixed pattern of up- and down-regulation six days after infection on sugar beets featuring variable levels of resistance compared to mycelia of the fungus grown in vitro.    Conclusions  The established  R. solani  AG2-2IIIB genome and EST sequences provide important information on the gene content, gene structure and transcriptional activity for this sugar beet pathogen. The enriched genomic platform provides an important platform to enhance our understanding of  R. solani  biology.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2561-1) contains supplementary material, which is available to authorized users.

Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes