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SRX1125367: Whole genome sequencing of Mycoplasma Pneumoniae : strain 3912
1 ILLUMINA (Illumina Genome Analyzer II) run: 680,328 spots, 129.3M bases, 82.2Mb downloads

Design: "Genomic DNA was collected using the Illustrabacteria genomic Kit (GE Healthcare) and sheared to 100 bp fragments using a Covaris S2 device. Paired-end Illumina libraries were created as described by Bentley et al. and the size selected to be between 200 and 400 bp. The resulting libraries were quantified on an Agilent Bioanalyzer chip (Agilent Technologies). Double-stranded templates were cluster amplified and sequenced on an Illumina GAII. Sequences were filtered according to quality, trimmed for the latest 5 bases ans subsampled to reach a coverage of about 150 times the genome of Mycoplasma pneumoniae M129"
Submitted by: Centre for genomic regulation (CRG)
Study: Genome sequencing and assembly of strains of Mycoplasma pneumoniae
show Abstracthide Abstract
The human respiratory tract pathogen M. pneumoniae is one of the best characterized minimal bacterium. Until now, two main groups of clinical isolates of this bacterium have been described (types 1 and 2), differing in the sequence of the P1 adhesin gene. Here, we have sequenced the genomes of 23 clinical isolates of M. pneumoniae. Studying SNPs, non-synonymous mutations, indels and genome rearrangements of these 23 strains and 4 previously sequenced ones, has revealed new subclasses in the two main groups, some of them being associated with the country of isolation. Integrative analysis of in vitro gene essentiality and mutation rates enabled the identification of several putative virulence factors and antigenic proteins; revealing recombination machinery, glycerol metabolism and peroxide production as possible factors in the genetics and physiology of these pathogenic strains. Additionally, the transcriptomes and proteomes of two representative strains, one from each of the two main groups, have been characterized to evaluate the impact of mutations on RNA and proteins levels. This study has revealed that type 2 strains show high expression levels of CARDs toxin, a protein recently shown to be one of the major factors of inflammation. Thus, we propose that type 2 strains are likely to be more virulent than type 1 strains.
Sample: sample 6
SAMN03897304 • SRS1017545 • All experiments • All runs
Library:
Name: 3912
Instrument: Illumina Genome Analyzer II
Strategy: WGS
Source: GENOMIC
Selection: unspecified
Layout: PAIRED
Spot descriptor:
forward96  reverse

Runs: 1 run, 680,328 spots, 129.3M bases, 82.2Mb
Run# of Spots# of BasesSizePublished
SRR2135835680,328129.3M82.2Mb2015-09-11

ID:
1641172

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