title: Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011.
abstract: The availability of next-generation sequences of transcripts from prokaryotic organisms offers the opportunity to design a new generation of automated genome annotation tools not yet available for prokaryotes. In this work, we designed EuGene-P, the first integrative prokaryotic gene finder tool which combines a variety of high-throughput data, including oriented RNA-Seq data, directly into the prediction process. This enables the automated prediction of coding sequences (CDSs), untranslated regions, transcription start sites (TSSs) and non-coding RNA (ncRNA, sense and antisense) genes. EuGene-P was used to comprehensively and accurately annotate the genome of the nitrogen-fixing bacterium Sinorhizobium meliloti strain 2011, leading to the prediction of 6308 CDSs as well as 1876 ncRNAs. Among them, 1280 appeared as antisense to a CDS, which supports recent findings that antisense transcription activity is widespread in bacteria. Moreover, 4077 TSSs upstream of protein-coding or non-coding genes were precisely mapped providing valuable data for the study of promoter regions. By looking for RpoE2-binding sites upstream of annotated TSSs, we were able to extend the S. meliloti RpoE2 regulon by ∼3-fold. Altogether, these observations demonstrate the power of EuGene-P to produce a reliable and high-resolution automatic annotation of prokaryotic genomes.
authors.affiliation: INRA, Laboratoire des Interactions Plantes-Microorganismes-LIPM, UMR 441, Castanet-Tolosan F-31326, France.
authors.forename: Erika
authors.initials: E
authors.lastname: Sallet
authors.forename: Brice
authors.initials: B
authors.lastname: Roux
authors.forename: Laurent
authors.initials: L
authors.lastname: Sauviac
authors.forename: Marie-Francoise
authors.initials: MF
authors.lastname: Jardinaud
authors.forename: Sébastien
authors.initials: S
authors.lastname: Carrère
authors.forename: Thomas
authors.initials: T
authors.lastname: Faraut
authors.forename: Fernanda
authors.initials: F
authors.lastname: de Carvalho-Niebel
authors.forename: Jérôme
authors.initials: J
authors.lastname: Gouzy
authors.forename: Pascal
authors.initials: P
authors.lastname: Gamas
authors.forename: Delphine
authors.initials: D
authors.lastname: Capela
authors.forename: Claude
authors.initials: C
authors.lastname: Bruand
authors.forename: Thomas
authors.initials: T
authors.lastname: Schiex
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D016680:Genome, Bacterial; D058977:Molecular Sequence Annotation / Q000379:methods*; D009586:Nitrogen Fixation / Q000235:genetics; D016366:Open Reading Frames; D022661:RNA, Untranslated / Q000235:genetics; D018085:Regulon; D012808:Sigma Factor / Q000235:genetics; D016962:Sinorhizobium meliloti / Q000235:genetics*; D012984:Software; D024363:Transcription Initiation Site
chemical_list: D022661:RNA, Untranslated; D012808:Sigma Factor; C063202:sporulation-specific sigma factors
keywords: RNA-Seq; genome annotation; prokaryotes; rhizobium