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High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic.

Sealfon R, Gire S, Ellis C, Calderwood S, Qadri F, Hensley L, Kellis M, Ryan ET, LaRocque RC, Harris JB, Sabeti PC - BMC Genomics (2012)

Bottom Line: Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants.We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads.Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA. rsealfon@mit.edu

ABSTRACT

Background: Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe cholera epidemic began in Haiti, with additional cases identified in the neighboring Dominican Republic. We used whole-genome approaches to sequence four Vibrio cholerae isolates from Haiti and the Dominican Republic and three additional V. cholerae isolates to a high depth of coverage (>2000x); four of the seven isolates were previously sequenced.

Results: Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants. We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads. Phylogenetic analysis between the newly sequenced and thirty-three previously sequenced V. cholerae isolates indicates that the Haitian and Dominican Republic isolates are closest to strains from South Asia. The Haitian and Dominican Republic isolates form a tight cluster, with only four variants unique to individual isolates. These variants are located in the CTX region, the SXT region, and the core genome. Of the 126 mutations identified that separate the Haiti-Dominican Republic cluster from the V. cholerae reference strain (N16961), 73 are non-synonymous changes, and a number of these changes cluster in specific genes and pathways.

Conclusions: Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

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Phylogeny of the sequenced strains and 33 previously sequenced V. cholerae isolates.  We constructed a maximum-likelihood phylogeny using RaxML based on genes conserved across all newly sequenced isolates as well as 33 previously sequenced V. cholerae  isolates. The isolates sequenced in our study are shown in red.
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Figure 3: Phylogeny of the sequenced strains and 33 previously sequenced V. cholerae isolates. We constructed a maximum-likelihood phylogeny using RaxML based on genes conserved across all newly sequenced isolates as well as 33 previously sequenced V. cholerae isolates. The isolates sequenced in our study are shown in red.

Mentions: The genomic content of the DB_2002 isolate is similar to that of other O139 serogroup isolates. Phylogenetic analysis indicates that DB_2002 clusters closely with an O139 serogroup isolate from India (MO10, [GenBank: AAKF03000000]) (Figure 3). The deletions in the superintegron, absence of the VPI-2 genomic island, presence of the SXT region, and differences in O antigen genes are characteristic of other O139-serogroup isolates [14,15].


High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic.

Sealfon R, Gire S, Ellis C, Calderwood S, Qadri F, Hensley L, Kellis M, Ryan ET, LaRocque RC, Harris JB, Sabeti PC - BMC Genomics (2012)

Phylogeny of the sequenced strains and 33 previously sequenced V. cholerae isolates.  We constructed a maximum-likelihood phylogeny using RaxML based on genes conserved across all newly sequenced isolates as well as 33 previously sequenced V. cholerae  isolates. The isolates sequenced in our study are shown in red.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473251&req=5

Figure 3: Phylogeny of the sequenced strains and 33 previously sequenced V. cholerae isolates. We constructed a maximum-likelihood phylogeny using RaxML based on genes conserved across all newly sequenced isolates as well as 33 previously sequenced V. cholerae isolates. The isolates sequenced in our study are shown in red.
Mentions: The genomic content of the DB_2002 isolate is similar to that of other O139 serogroup isolates. Phylogenetic analysis indicates that DB_2002 clusters closely with an O139 serogroup isolate from India (MO10, [GenBank: AAKF03000000]) (Figure 3). The deletions in the superintegron, absence of the VPI-2 genomic island, presence of the SXT region, and differences in O antigen genes are characteristic of other O139-serogroup isolates [14,15].

Bottom Line: Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants.We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads.Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA. rsealfon@mit.edu

ABSTRACT

Background: Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe cholera epidemic began in Haiti, with additional cases identified in the neighboring Dominican Republic. We used whole-genome approaches to sequence four Vibrio cholerae isolates from Haiti and the Dominican Republic and three additional V. cholerae isolates to a high depth of coverage (>2000x); four of the seven isolates were previously sequenced.

Results: Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants. We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads. Phylogenetic analysis between the newly sequenced and thirty-three previously sequenced V. cholerae isolates indicates that the Haitian and Dominican Republic isolates are closest to strains from South Asia. The Haitian and Dominican Republic isolates form a tight cluster, with only four variants unique to individual isolates. These variants are located in the CTX region, the SXT region, and the core genome. Of the 126 mutations identified that separate the Haiti-Dominican Republic cluster from the V. cholerae reference strain (N16961), 73 are non-synonymous changes, and a number of these changes cluster in specific genes and pathways.

Conclusions: Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

Show MeSH
Related in: MedlinePlus