Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011

DNA Res. 2013 Aug;20(4):339-54. doi: 10.1093/dnares/dst014. Epub 2013 Apr 18.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping / methods*
  • Genome, Bacterial*
  • Molecular Sequence Annotation / methods*
  • Nitrogen Fixation / genetics
  • Open Reading Frames
  • RNA, Untranslated / genetics
  • Regulon*
  • Sigma Factor / genetics
  • Sinorhizobium meliloti / genetics*
  • Software*
  • Transcription Initiation Site


  • RNA, Untranslated
  • Sigma Factor
  • sporulation-specific sigma factors