Abstract
BackgroundSugar 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.ResultsThe 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.ConclusionsThe 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 materialThe online version of this article (doi:10.1186/s12864-016-2561-1) contains supplementary material, which is available to authorized users.
Highlights
Sugar beet (Beta vulgaris) is a crop cultivated for its high content in sugar, but it is vulnerable to many soil-borne pathogens
The enriched genomic platform provides an important platform to enhance our understanding of R. solani biology
The R. solani AG2-2IIIB draft genome sequence The draft genome sequence of the R. solani AG2-2IIIB isolate BBA 69670 was established by high-throughput sequencing on the Illumina MiSeq system
Summary
Sugar beet (Beta vulgaris) is a crop cultivated for its high content in sugar, but it is vulnerable to many soil-borne pathogens. Vulgaris) is a crop grown in temperate geographic regions for its high sugar content in the root, which accounts for about 30 % of the sugar production in the world This species is one of our youngest cultivated crop plants whereupon work on crop improvements started in the mid-1800s and was enhanced after World War II [1]. Rhizoctonia solani (telemorph: Thanatephorus cucumeris) is one of them This anamorphic basidiomycete fungus has a wide host range causing disease on more than 200 plant species [3, 4]. The fungus causes dark lesions on roots, when attacking somewhat older plants; these symptoms develop into rotted root tissue as the disease progresses
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