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CAMBer: an approach to support comparative analysis of multiple bacterial strains.

ABSTRACT: BACKGROUND: There is a large amount of inconsistency in gene structure annotations of bacterial strains. This inconsistency is a frustrating impedance to effective comparative genomic analysis of bacterial strains in promising applications such as gaining insights into bacterial drug resistance. RESULTS: Here, we propose CAMBer as an approach to support comparative analysis of multiple bacterial strains. CAMBer produces what we called multigene families. Each multigene family reveals genes that are in one-to-one correspondence in the bacterial strains, thereby permitting their annotations to be integrated. We present results of our method applied to three human pathogens: Escherichia coli, Mycobacterium tuberculosis and Staphylococcus aureus. CONCLUSIONS: As a result, more accurate and more comprehensive annotations of the bacterial strains can be produced.

SUBMITTER: Wozniak M

PROVIDER: S-EPMC3194237 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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CAMBer: an approach to support comparative analysis of multiple bacterial strains.

Wozniak Michal M Wong Limsoon L Tiuryn Jerzy J

BMC genomics 20110727

<h4>Background</h4>There is a large amount of inconsistency in gene structure annotations of bacterial strains. This inconsistency is a frustrating impedance to effective comparative genomic analysis of bacterial strains in promising applications such as gaining insights into bacterial drug resistance.<h4>Results</h4>Here, we propose CAMBer as an approach to support comparative analysis of multiple bacterial strains. CAMBer produces what we called multigene families. Each multigene family reveal ...[more]

PMID: 21989220

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Project description:BackgroundThe Gram-negative intracellular bacterium Mycoplasma anatis is a pathogen of respiratory infectious diseases in ducks and has caused significant economic losses in the poultry industry.ObjectiveThis study, as the first report of the structure and function of the pan-genome of Mycoplasma anatis, may provide a valuable genetic basis for many aspects of future research on the pathogens of waterfowl.MethodsWe sequenced the whole genomes of 15 Mycoplasma anatis isolated from ducks in China. Draft genome sequencing was carried out and whole-genome sequencing was performed by the sequencers of the PacBio Sequel and an IonTorrent Personal Genome Machine (PGM). Then the common genic elements of protein-coding genes, tRNAs, and rRNAs of Mycoplasma anatis genomes were predicted by using the pipeline Prokka v1.13.7. To investigate homologous protein clusters across Mycoplasma anatis genomes, we adopted Roary v3.13.0 to cluster orthologous genes (OGs) based on the following criteria.ResultsWe obtained one complete genome and 14 genome sketches. Microbial mobile genetic element analysis revealed the distribution of insertion sequences (IS30, IS3, and IS1634), prophage regions, and CRISPR arrays in the genome of Mycoplasma anatis. Comparative genomic analysis decoded the genetic components and functional classification of the pan-genome of Mycoplasma anatis that comprised 646 core genes, 231 dispensable genes and among them 110 was strain-specific. Virulence-related gene profiles of Mycoplasma anatis were systematically identified, and the products of these genes included bacterial ABC transporter systems, iron transport proteins, toxins, and secretion systems.ConclusionA complete virulence-related gene profile of Mycoplasma anatis has been identified, most of the genes are highly conserved in all strains. Sequencing results are relevant to the molecular mechanisms of drug resistance, adaptive evolution of pathogens, population structure, and vaccine development.

Dataset Information

CAMBer: an approach to support comparative analysis of multiple bacterial strains.

Publications

CAMBer: an approach to support comparative analysis of multiple bacterial strains.

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