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Title: Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity

Abstract

Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V. cholerae in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of V. cholerae strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 V. cholerae, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that V. cholerae has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in V. cholerae. We also found pervasive chromosomalmore » rearrangements such as duplications and indels in many strains. The majority of Vibrio genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel V. cholerae non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [2];  [2];  [3];  [1];  [4];  [5];  [4];  [1];  [6]
  1. Henry M. Jackson Foundation, Bethesda, MD (United States); Naval Medical Research Center-Frederick, Fort Detrick, MD (United States)
  2. OpGen, Inc., Gaithersburg, MD (United States)
  3. Univ. of Florida, Gainesville, FL (United States)
  4. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  5. Naval Medical Research Center-Frederick, Fort Detrick, MD (United States)
  6. United States Army Medical Research Institute for Infectious Diseases, Frederick, MD (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1193714
Alternate Identifier(s):
OSTI ID: 1214728
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 10; Journal Issue: 3; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; vibrio cholerae; chromosomes; genomic databases; comparative genomics; chromosome mapping; cholera; genome complexity; sequence databases

Citation Formats

Chapman, Carol, Henry, Matthew, Bishop-Lilly, Kimberly A., Awosika, Joy, Briska, Adam, Ptashkin, Ryan N., Wagner, Trevor, Rajanna, Chythanya, Tsang, Hsinyi, Johnson, Shannon L., Mokashi, Vishwesh P., Chain, Patrick S. G., Sozhamannan, Shanmuga, and Minogue, Timothy D. Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity. United States: N. p., 2015. Web. doi:10.1371/journal.pone.0120311.
Chapman, Carol, Henry, Matthew, Bishop-Lilly, Kimberly A., Awosika, Joy, Briska, Adam, Ptashkin, Ryan N., Wagner, Trevor, Rajanna, Chythanya, Tsang, Hsinyi, Johnson, Shannon L., Mokashi, Vishwesh P., Chain, Patrick S. G., Sozhamannan, Shanmuga, & Minogue, Timothy D. Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity. United States. doi:10.1371/journal.pone.0120311.
Chapman, Carol, Henry, Matthew, Bishop-Lilly, Kimberly A., Awosika, Joy, Briska, Adam, Ptashkin, Ryan N., Wagner, Trevor, Rajanna, Chythanya, Tsang, Hsinyi, Johnson, Shannon L., Mokashi, Vishwesh P., Chain, Patrick S. G., Sozhamannan, Shanmuga, and Minogue, Timothy D. Fri . "Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity". United States. doi:10.1371/journal.pone.0120311. https://www.osti.gov/servlets/purl/1193714.
@article{osti_1193714,
title = {Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity},
author = {Chapman, Carol and Henry, Matthew and Bishop-Lilly, Kimberly A. and Awosika, Joy and Briska, Adam and Ptashkin, Ryan N. and Wagner, Trevor and Rajanna, Chythanya and Tsang, Hsinyi and Johnson, Shannon L. and Mokashi, Vishwesh P. and Chain, Patrick S. G. and Sozhamannan, Shanmuga and Minogue, Timothy D.},
abstractNote = {Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V. cholerae in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of V. cholerae strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 V. cholerae, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that V. cholerae has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in V. cholerae. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of Vibrio genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel V. cholerae non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.},
doi = {10.1371/journal.pone.0120311},
journal = {PLoS ONE},
number = 3,
volume = 10,
place = {United States},
year = {Fri Mar 20 00:00:00 EDT 2015},
month = {Fri Mar 20 00:00:00 EDT 2015}
}

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