Abstract
Rhizoctonia solani, a soil-born plant pathogenic basidiomycetous fungus, affects various economically important agricultural and horticultural crops. The draft genome sequence for the R. solani AG1-IB isolate 7/3/14 as well as a corresponding transcriptome dataset (Expressed Sequence Tags—ESTs) were established previously. Development of a specific R. solani AG1-IB gene model based on GMAP transcript mapping within the eukaryotic gene prediction platform AUGUSTUS allowed detection of new genes and provided insights into the gene structure of this fungus. In total, 12,616 genes were recognized in the genome of the AG1-IB isolate. Analysis of predicted genes by means of different bioinformatics tools revealed new genes whose products potentially are involved in degradation of plant cell wall components, melanin formation and synthesis of secondary metabolites. Comparative genome analyses between members of different R. solani anastomosis groups, namely AG1-IA, AG3 and AG8 and the newly annotated R. solani AG1-IB genome were performed within the comparative genomics platform EDGAR. It appeared that only 21 to 28% of all genes encoded in the draft genomes of the different strains were identified as core genes. Based on Average Nucleotide Identity (ANI) and Average Amino-acid Identity (AAI) analyses, considerable sequence differences between isolates representing different anastomosis groups were identified. However, R. solani isolates form a distinct cluster in relation to other fungi of the phylum Basidiomycota. The isolate representing AG1-IB encodes significant more genes featuring predictable functions in secondary metabolite production compared to other completely sequenced R. solani strains. The newly established R. solani AG1-IB 7/3/14 gene layout now provides a reliable basis for post-genomics studies.
Highlights
The basidiomycetous fungus Rhizoctonia solani Kühn is a worldwide prevalent soil-borne plant pathogen
Likewise, Expressed Sequence Tags (ESTs) were deeply sequenced for this R. solani isolate grown in different media [8]
These sequence datasets were used to deduce an R. solani specific gene model which was applied to uncover new R. solani AG1-IB genes that were missed in previous gene predictions on genomic contigs or are not Comparative Genomics of Rhizoctonia solani represented in the EST datasets
Summary
The basidiomycetous fungus Rhizoctonia solani Kühn (teleomorph Thanatephorus cucumeris [Frank] Donk) is a worldwide prevalent soil-borne plant pathogen. It causes diseases on many economically important crops including sugar beet, potato, wheat, rape, maize, soybean, rice, cabbage, cauliflower, tomato and lettuce as well as ornamental plants and forest trees [1]. The genome sequences for AG3 and AG8 isolates became available quite recently [6,7]. The R. solani AG1-IB genome project provided first insights into the genome size and structure, gene content and functional annotation of the sequenced isolate. R. solani ESTs provided information on genes transcribed under the conditions tested and their exon structure. Putative pathogenicity determinants were recognized within the EST dataset
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