Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011.
DNA Res, 2013/8;20(4):339-54.
Sallet E[1], Roux B, Sauviac L, Jardinaud MF, Carrère S, Faraut T, de Carvalho-Niebel F, Gouzy J, Gamas P, Capela D, Bruand C, Schiex T
Affiliations
PMID: 23599422DOI: 10.1093/dnares/dst014
Impact factor: 4.477
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.
Keywords: RNA-Seq; genome annotation; prokaryotes; rhizobium
MeSH terms
Chromosome Mapping; Genome, Bacterial; Molecular Sequence Annotation; Nitrogen Fixation; Open Reading Frames; RNA, Untranslated; Regulon; Sigma Factor; Sinorhizobium meliloti; Software; Transcription Initiation Site
More resources
Full text:
Europe PubMed Central; PubMed Central
EndNote: Download