title: Comparative Transcriptome Analysis between the Fungal Plant Pathogens Sclerotinia sclerotiorum and S. trifoliorum Using RNA Sequencing.
abstract: The fungal plant pathogens Sclerotinia sclerotiorum and S. trifoliorum are morphologically similar, but differ considerably in host range. In an effort to elucidate mechanisms of the host range difference, transcriptomes of the 2 species at vegetative growth stage were compared to gain further insight into commonality and uniqueness in gene expression and pathogenic mechanisms of the 2 closely related pathogens. A total of 23133 and 21043 unique transcripts were obtained from S. sclerotiorum and S. trifoliorum, respectively. Approximately 43% of the transcripts were genes with known functions for both species. Among 1411 orthologous contigs, about 10% (147) were more highly (>3-fold) expressed in S. trifoliorum than in S. sclerotiorum, and about 12% (173) of the orthologs were more highly (>3-fold) expressed in S. sclerotiorum than in S. trifoliorum. The expression levels of genes on the supercontig 30 have the highest correlation coefficient value between the 2 species. Twenty-seven contigs were found to be new and unique for S. trifoliorum. Additionally, differences in expressed genes involved in pathogenesis like oxalate biosynthesis and endopolygalacturonases were detected between the 2 species. The analyses of the transcriptomes not only discovered similarities and uniqueness in gene expression between the 2 closely related species, providing additional information for annotation the S. sclerotiorum genome, but also provided foundation for comparing the transcriptomes with host-infecting transcriptomes.
authors.affiliation: From the Department of Plant Pathology, Washington State University, Pullman, WA 99164 (Qiu and Xu); and Grain Legume Genetics and Physiology Research, USDA-ARS, Washington State University, Pullman, WA 99164 (Vandemark and Chen). Dan Qiu is now at the Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211.
authors.forename: Dan
authors.initials: D
authors.lastname: Qiu
authors.affiliation: From the Department of Plant Pathology, Washington State University, Pullman, WA 99164 (Qiu and Xu); and Grain Legume Genetics and Physiology Research, USDA-ARS, Washington State University, Pullman, WA 99164 (Vandemark and Chen). Dan Qiu is now at the Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211.
authors.forename: Liangsheng
authors.initials: L
authors.lastname: Xu
authors.affiliation: From the Department of Plant Pathology, Washington State University, Pullman, WA 99164 (Qiu and Xu); and Grain Legume Genetics and Physiology Research, USDA-ARS, Washington State University, Pullman, WA 99164 (Vandemark and Chen). Dan Qiu is now at the Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211.
authors.forename: George
authors.initials: G
authors.lastname: Vandemark
authors.affiliation: From the Department of Plant Pathology, Washington State University, Pullman, WA 99164 (Qiu and Xu); and Grain Legume Genetics and Physiology Research, USDA-ARS, Washington State University, Pullman, WA 99164 (Vandemark and Chen). Dan Qiu is now at the Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211. w-chen@wsu.edu.
authors.forename: Weidong
authors.initials: W
authors.lastname: Chen
mesh_terms: D001203:Ascomycota / Q000145:classification / Q000235:genetics*; D020451:Contig Mapping; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D005800:Genes, Fungal; D010935:Plant Diseases / Q000382:microbiology; D012331:RNA, Fungal / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D012331:RNA, Fungal
keywords: RNA sequencing; S. trifoliorum; Sclerotinia sclerotiorum; transcriptome