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Analysis of Multiple Brachyspira hyodysenteriae Genomes Confirms That the Species Is Relatively Conserved but Has Potentially Important Strain Variation.

Black M, Moolhuijzen P, Barrero R, La T, Phillips N, Hampson D, Herbst W, Barth S, Bellgard M - PLoS ONE (2015)

Bottom Line: The result is a global comparative genomic analysis of B. hyodysenteriae genomes revealing potential differential phenotypic markers for numerous strains.Despite the differences found, the genomes were less varied than those of the related pathogenic species Brachyspira pilosicoli, and the analysis supports the clonal nature of the species.This is the first intra-species B. hyodysenteriae comparative genomic analysis.

View Article: PubMed Central - PubMed

Affiliation: Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia, Australia.

ABSTRACT
The intestinal spirochete Brachyspira hyodysenteriae is an important pathogen in swine, causing mucohemorrhagic colitis in a disease known as swine dysentery. Based on the detection of significant linkage disequilibrium in multilocus sequence data, the species is considered to be clonal. An analysis of the genome sequence of Western Australian B. hyodysenteriae strain WA1 has been published, and in the current study 19 further strains from countries around the world were sequenced with Illumina technology. The genomes were assembled and aligned to over 97.5% of the reference WA1 genome at a percentage sequence identity better than 80%. Strain regions not aligned to the reference ranged between 0.2 and 2.5%. Clustering of the strain genes found on average 2,354 (88%) core genes, 255 (8.6%) ancillary genes and 77 (2.9%) unique genes per strain. Depending on the strain the proportion of genes with 100% sequence identity to WA1 ranged from 85% to 20%. The result is a global comparative genomic analysis of B. hyodysenteriae genomes revealing potential differential phenotypic markers for numerous strains. Despite the differences found, the genomes were less varied than those of the related pathogenic species Brachyspira pilosicoli, and the analysis supports the clonal nature of the species. From this study, a public genome resource has been created that will serve as a repository for further genetic and phenotypic studies of these important porcine bacteria. This is the first intra-species B. hyodysenteriae comparative genomic analysis.

No MeSH data available.


Related in: MedlinePlus

Gene alignments (shown in blue) of strains at better than 90% nucleotide sequence identity and 90% coverage to the reference NC_012225 3Mb genome.Strain labels are color-coded, Australia (red), Japan and Korea (black), Europe (blue), North America (green) and Unknown (grey). The sub-cluster of four Australian strains with high sequence identity is boxed.
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pone.0131050.g001: Gene alignments (shown in blue) of strains at better than 90% nucleotide sequence identity and 90% coverage to the reference NC_012225 3Mb genome.Strain labels are color-coded, Australia (red), Japan and Korea (black), Europe (blue), North America (green) and Unknown (grey). The sub-cluster of four Australian strains with high sequence identity is boxed.

Mentions: The predicted strain gene alignment to the WA1 reference is shown in Fig 1. The closest strains by sequence identity to the WA1 reference were Queensland strain Q17 and New South Wales strain NSW5. No relatedness due to geographic location could be established. A region of approximately 24 Kb with variable gene alignments with the reference strain genes was identified at reference genomic position 1,501 Kb to 1,525 Kb. The gene content of this region included a type IIS restriction /modification enzyme, hypothetical proteins, a bipolar DNA helicase HerA, and a mobile element protein (Fig 2).


Analysis of Multiple Brachyspira hyodysenteriae Genomes Confirms That the Species Is Relatively Conserved but Has Potentially Important Strain Variation.

Black M, Moolhuijzen P, Barrero R, La T, Phillips N, Hampson D, Herbst W, Barth S, Bellgard M - PLoS ONE (2015)

Gene alignments (shown in blue) of strains at better than 90% nucleotide sequence identity and 90% coverage to the reference NC_012225 3Mb genome.Strain labels are color-coded, Australia (red), Japan and Korea (black), Europe (blue), North America (green) and Unknown (grey). The sub-cluster of four Australian strains with high sequence identity is boxed.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4476648&req=5

pone.0131050.g001: Gene alignments (shown in blue) of strains at better than 90% nucleotide sequence identity and 90% coverage to the reference NC_012225 3Mb genome.Strain labels are color-coded, Australia (red), Japan and Korea (black), Europe (blue), North America (green) and Unknown (grey). The sub-cluster of four Australian strains with high sequence identity is boxed.
Mentions: The predicted strain gene alignment to the WA1 reference is shown in Fig 1. The closest strains by sequence identity to the WA1 reference were Queensland strain Q17 and New South Wales strain NSW5. No relatedness due to geographic location could be established. A region of approximately 24 Kb with variable gene alignments with the reference strain genes was identified at reference genomic position 1,501 Kb to 1,525 Kb. The gene content of this region included a type IIS restriction /modification enzyme, hypothetical proteins, a bipolar DNA helicase HerA, and a mobile element protein (Fig 2).

Bottom Line: The result is a global comparative genomic analysis of B. hyodysenteriae genomes revealing potential differential phenotypic markers for numerous strains.Despite the differences found, the genomes were less varied than those of the related pathogenic species Brachyspira pilosicoli, and the analysis supports the clonal nature of the species.This is the first intra-species B. hyodysenteriae comparative genomic analysis.

View Article: PubMed Central - PubMed

Affiliation: Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia, Australia.

ABSTRACT
The intestinal spirochete Brachyspira hyodysenteriae is an important pathogen in swine, causing mucohemorrhagic colitis in a disease known as swine dysentery. Based on the detection of significant linkage disequilibrium in multilocus sequence data, the species is considered to be clonal. An analysis of the genome sequence of Western Australian B. hyodysenteriae strain WA1 has been published, and in the current study 19 further strains from countries around the world were sequenced with Illumina technology. The genomes were assembled and aligned to over 97.5% of the reference WA1 genome at a percentage sequence identity better than 80%. Strain regions not aligned to the reference ranged between 0.2 and 2.5%. Clustering of the strain genes found on average 2,354 (88%) core genes, 255 (8.6%) ancillary genes and 77 (2.9%) unique genes per strain. Depending on the strain the proportion of genes with 100% sequence identity to WA1 ranged from 85% to 20%. The result is a global comparative genomic analysis of B. hyodysenteriae genomes revealing potential differential phenotypic markers for numerous strains. Despite the differences found, the genomes were less varied than those of the related pathogenic species Brachyspira pilosicoli, and the analysis supports the clonal nature of the species. From this study, a public genome resource has been created that will serve as a repository for further genetic and phenotypic studies of these important porcine bacteria. This is the first intra-species B. hyodysenteriae comparative genomic analysis.

No MeSH data available.


Related in: MedlinePlus