Comparative genomic analysis of 93 Bp strains using K96243 as the reference
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PROVIDER: PRJNA103275 | ENA |
REPOSITORIES: ENA
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Project description:Natural isolates of Burkholderia pseudomallei (Bp), the causative agent of melioidosis, are known to exhibit diverse phenotypic traits, suggesting significant intraspecies genetic heterogeneity. Using whole-genome Bp microarrays, we experimentally mapped patterns of large-scale genomic variation in 93 South East Asian clinical, environmental, and animal Bp isolates. 14% of the reference Bp K96243 genome was variably present across the strain panel, more than double previous estimates, and both hypothetical proteins and paralogous gene pairs (PGPs) were significantly over-represented in the set of strain-variable genes. Examining patterns of PGP retention and loss, we successfully sub-categorized the PGPs into non-redundant, functionally biased, and completely redundant classes. We then identified 20 novel regions (“islands”) variably present between strains previously missed by computational analysis. Three of these novel islands contained lipopolysaccharide (LPS) biosynthesis genes, and strains lacking one such LPS island demonstrated reduced virulence in mouse infection assays. Clinical isolates associated with human melioidosis were strongly associated with the presence of specific genomic islands, but a common set of virulence-related genes was present in all strains. Our results suggest that most Bp strains possess a core virulence machinery capable of causing disease, but accessory functions provided by mobile elements may predispose distinct host species and ecological niches to specific individual strains. This hierarchical model of Bp virulence reconciles previous conflicting studies comparing Bp environmental and clinical isolates, and suggests novel molecular strategies for disease surveillance and outbreak detection efforts in melioidosis. Keywords: aCGH of 93 Bp strains
2008-12-26 | GSE9491 | GEO
Project description:Natural isolates of Burkholderia pseudomallei (Bp), the causative agent of melioidosis, are known to exhibit diverse phenotypic traits, suggesting significant intraspecies genetic heterogeneity. Using whole-genome Bp microarrays, we experimentally mapped patterns of large-scale genomic variation in 93 South East Asian clinical, environmental, and animal Bp isolates. 14% of the reference Bp K96243 genome was variably present across the strain panel, more than double previous estimates, and both hypothetical proteins and paralogous gene pairs (PGPs) were significantly over-represented in the set of strain-variable genes. Examining patterns of PGP retention and loss, we successfully sub-categorized the PGPs into non-redundant, functionally biased, and completely redundant classes. We then identified 20 novel regions (âislandsâ) variably present between strains previously missed by computational analysis. Three of these novel islands contained lipopolysaccharide (LPS) biosynthesis genes, and strains lacking one such LPS island demonstrated reduced virulence in mouse infection assays. Clinical isolates associated with human melioidosis were strongly associated with the presence of specific genomic islands, but a common set of virulence-related genes was present in all strains. Our results suggest that most Bp strains possess a core virulence machinery capable of causing disease, but accessory functions provided by mobile elements may predispose distinct host species and ecological niches to specific individual strains. This hierarchical model of Bp virulence reconciles previous conflicting studies comparing Bp environmental and clinical isolates, and suggests novel molecular strategies for disease surveillance and outbreak detection efforts in melioidosis. Keywords: aCGH of 93 Bp strains genomic DNA of 93 Bp strains were assessed on Bp_array_v2
2008-12-25 | E-GEOD-9491 | biostudies-arrayexpress
Project description:Burkholderia pseudomallei K96243 re-sequencing
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Project description:Burkholderia pseudomallei K96243 Genome sequencing
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Project description:To use whole genome microarrays to compare the differences in genome contents of 5 B. pseudomallei isolated from clinical specimens and environmental sample with B. pseudomallei K96243 reference strain and reveals variable patterns of Genomic Islands (GIs) Keywords: Comparative genomic hybridization DNA microarrays were used to compare genome of clinical and environmental B. pseudomallei isolates with B. pseudomallei K96243 reference strain (B. pseudomallei K96243 vs. B. pseudmallei isolates). Each hybridization was used for comparison between B. pseudomallei K96243 as a reference strain with environmental isolate BP45s, environmental isolate BP28L, clinical isolate H307, clinical isolate P54, clinical isolate P82. Two replicate per array. Multiple hits with 90-99.99 % identity correspond to other locus are replicate of their genes were averaged and analyzed.
2012-07-30 | E-GEOD-19558 | biostudies-arrayexpress
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Project description:To use whole genome microarrays to compare the differences in genome contents of 5 B. pseudomallei isolated from clinical specimens and environmental sample with B. pseudomallei K96243 reference strain and reveals variable patterns of Genomic Islands (GIs) Keywords: Comparative genomic hybridization
2012-07-31 | GSE19558 | GEO
Project description:Microarray-based comparative genomic hybridizations were used to estimate whole genomic diversity of representative Actinobacillus pleuropneumoniae strains. Our goal was to identify conserved genes, especially those predicted to encode outer membrane proteins and lipoproteins because of their potential for the development of more effective vaccines. Keywords: Comparative Genomic Hybridisation
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