title: dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42.
abstract: Bacillus amyloliquefaciens subsp. plantarum FZB42 is a representative of Gram-positive plant-growth-promoting rhizobacteria (PGPR) that inhabit plant root environments. In order to better understand the molecular mechanisms of bacteria-plant symbiosis, we have systematically analyzed the primary transcriptome of strain FZB42 grown under rhizosphere-mimicking conditions using differential RNA sequencing (dRNA-seq). Our analysis revealed 4,877 transcription start sites for protein-coding genes, identified genes differentially expressed under different growth conditions, and corrected many previously mis-annotated genes. We also identified a large number of riboswitches and cis-encoded antisense RNAs, as well as trans-encoded small noncoding RNAs that may play important roles in the gene regulation of Bacillus. Overall, our analyses provided a landscape of Bacillus primary transcriptome and improved the knowledge of rhizobacteria-host interactions.
authors.affiliation: Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China.
authors.forename: Ben
authors.initials: B
authors.lastname: Fan
authors.affiliation: RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.affiliation: RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
authors.forename: Yanjie
authors.initials: Y
authors.lastname: Chao
authors.affiliation: RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
authors.forename: Konrad
authors.initials: K
authors.lastname: Förstner
authors.affiliation: RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
authors.affiliation: Fachgebiet Phytomedizin, Albrecht Daniel Thaer Institut für Agrar- und Gartenbauwissenschaften, Lebenswissenschaftliche Fakultät, Humboldt Universität zu Berlin, 14195 Berlin, Germany.
authors.forename: Rainer
authors.initials: R
authors.lastname: Borriss
authors.affiliation: Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China.
authors.forename: Xiao-Qin
authors.initials: XQ
authors.lastname: Wu
mesh_terms: D001407:Bacillus / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D018517:Plant Roots / Q000382:microbiology*; D010944:Plants / Q000382:microbiology*; D022661:RNA, Untranslated / Q000235:genetics*; D012231:Rhizobium / Q000235:genetics*; D058441:Rhizosphere; D017423:Sequence Analysis, RNA / Q000379:methods; D013559:Symbiosis / Q000235:genetics; D024363:Transcription Initiation Site / Q000502:physiology; D059467:Transcriptome / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D022661:RNA, Untranslated