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Next Generation Annotation of prokarotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011

ABSTRACT: Next Generation Annotation of prokarotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011

OTHER RELATED OMICS DATASETS IN: GSE44083

PROVIDER: PRJNA188524 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR701979_1.fastq.gz	Fastqsanger.gz
	SRR701979_2.fastq.gz	Fastqsanger.gz
	SRR701980_1.fastq.gz	Fastqsanger.gz
	SRR701980_2.fastq.gz	Fastqsanger.gz
	SRR701981_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Next Generation Annotation of prokarotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011

Project description: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.

2013-04-01 | GSE44083 | GEO

Sinorhizobium meliloti 2011

Project description:Sinorhizobium meliloti 2011 Genome sequencing

| PRJNA187276 | ENA

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

Project description: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.

| S-EPMC3738161 | biostudies-literature

Sinorhizobium meliloti 2011

Project description:Sinorhizobium meliloti 2011 methylation detection - Rm2011-GD-ZIII-1 epigenomics

| PRJNA582353 | ENA

Sinorhizobium meliloti 2011

Project description:Sinorhizobium meliloti 2011 methylation detection - Rm2011-GD-ZII-1 epigenomics

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Sinorhizobium meliloti 2011

Project description:Sinorhizobium meliloti 2011 methylation detection - Rm2011-GD-FL-1 epigenomics

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Sinorhizobium meliloti 2011

Project description:Sinorhizobium meliloti 2011 methylation detection - BM908-GD-FL-3 epigenomics

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Sinorhizobium meliloti 2011

Project description:Sinorhizobium meliloti 2011 methylation detection - Rm2011-GD-Ms-1 epigenomics

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Project description:Sinorhizobium meliloti 2011 methylation detection - Rm2011-GD-FL-2 epigenomics

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