title: Transcriptome analysis of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 applying high-throughput sequencing of expressed sequence tags (ESTs).
abstract: 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.
authors.affiliation: Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Wibberg
authors.affiliation: Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany.
authors.forename: Lukas
authors.initials: L
authors.lastname: Jelonek
authors.affiliation: Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Rupp
authors.affiliation: Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Kröber
authors.affiliation: Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.affiliation: Leibniz-Institute of Vegetables and Ornamental Crops (IGZ), D-14979 Großbeeren, Germany.
authors.forename: Rita
authors.initials: R
authors.lastname: Grosch
authors.affiliation: Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.affiliation: Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany. Electronic address: aschluet@CeBiTec.Uni-Bielefeld.de.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schlüter
mesh_terms: D019295:Computational Biology; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D012232:Rhizoctonia / Q000235:genetics*
keywords: Antibiotics; Laccase; Plant cell wall digestive enzymes; Plant pathogenic fungus; cDNA