Next Generation Annotation of prokarotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011
With a view to re-annotate the genome sequence of the nitrogen fixing bacterium Sinorhizobium meliloti, we generated oriented sequences of transcripts. To cover a large number of expressed genes we prepared RNA from bacteria grown in three very different physiological conditions including bacteria grown in liquid cultures (in both exponential and stationary growth phases) and from 10-day-old nodules in which bacteria were differentiated in nitrogen fixing bacteroids. The transcripts sequences were then integrated into EuGene-P, a new prokaryotic genome annotation tool able to integrate high throughput data including oriented RNA-Seq data directly into the prediction process, which led to the production of an accurate and complete annotation of the genome of S. meliloti strain 2011. Overall design: 18 samples corresponding to bacteria in 3 different conditions. For each condition, both short and long RNA fractions were analyzed, and three replicates per condition and per RNA fraction were performed.