Transcriptome analysis of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 applying high-throughput sequencing of expressed sequence tags (ESTs)

• Published in: Fungal biology 2014-09, Vol.118 (9-10), p.800-813
• Main Authors: Wibberg, Daniel, Jelonek, Lukas, Rupp, Oliver, Kröber, Magdalena, Goesmann, Alexander, Grosch, Rita, Pühler, Alfred, Schlüter, Andreas
• Format: Article
• Language: English
• Subjects: Antibiotics; cDNA; Computational Biology; Expressed Sequence Tags; Gene Expression Profiling - methods; High-Throughput Nucleotide Sequencing; Laccase; Plant cell wall digestive enzymes; Plant pathogenic fungus; Rhizoctonia - genetics
• ISSN: 1878-6146; 1878-6162
• DOI: 10.1016/j.funbio.2014.06.007

Rhizoctonia solani is a soil-borne plant pathogenic fungus of the phylum Basidiomycota. It affects a wide range of agriculturally important crops and hence is responsible for economically relevant crop losses. Transcriptome analysis of the bottom rot pathogen R. solani AG1-1B (isolate 7/3/14) by applying high-throughput sequencing and bioinformatics methods addressing Expressed Sequence Tag (EST) data interpretation provided new insights in expressed genes of this fungus. Two normalized cDNA libraries representing different cultivation conditions of the fungus were sequenced on the 454 FLX (Roche) system. Subsequent to cDNA sequence assembly and quality control, ESTs were analysed applying advanced bioinformatics methods. More than 14 000 transcript isoforms originating from approximately 10 000 predictable R. solani AG1-IB 7/3/14 genes are represented in each dataset. Comparative analyses revealed several differentially expressed genes depending on the growth conditions applied. Determinants with predicted functions in recognition processes between the fungus and the host plant were identified. Moreover, many R. solani AG1-IB ESTs were predicted to encode putative cellulose, pectin, and lignin degrading enzymes. Furthermore, genes playing a possible role in mitogen-activated protein (MAP) kinase cascades, 4-aminobutyric acid (GABA) metabolism, melanin synthesis, plant defence antagonism, phytotoxin, and mycotoxin synthesis were detected. •Transcriptome analysis of the bottom rot pathogen R. solani AG1-1B (isolate 7/3/14).•More than 14 000 transcript isoforms representing approx. 10 000 predictable R. solani genes.•Identification of ESTs with predicted functions in recognition processes between the fungus and the host plant.•R. solani ESTs homologous to Ste12 and FMK1 were identified.•ESTs with predicted roles in cellulose, pectin and lignin degradation were identified.