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 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.
authors: Henry M. Jackson Foundation, Bethesda, Maryland, United States of America; Naval Medical Research Center-Frederick, Fort Detrick, Maryland, United States of America.
authors: Carol
authors: C
authors: Chapman
authors: Henry M. Jackson Foundation, Bethesda, Maryland, United States of America; Naval Medical Research Center-Frederick, Fort Detrick, Maryland, United States of America.
authors: Matthew
authors: M
authors: Henry
authors: Henry M. Jackson Foundation, Bethesda, Maryland, United States of America; Naval Medical Research Center-Frederick, Fort Detrick, Maryland, United States of America.
authors: Kimberly A
authors: KA
authors: Bishop-Lilly
authors: Henry M. Jackson Foundation, Bethesda, Maryland, United States of America; Naval Medical Research Center-Frederick, Fort Detrick, Maryland, United States of America.
authors: Joy
authors: J
authors: Awosika
authors: OpGen, Inc., Gaithersburg, Maryland, United States of America.
authors: Adam
authors: A
authors: Briska
authors: OpGen, Inc., Gaithersburg, Maryland, United States of America.
authors: Ryan N
authors: RN
authors: Ptashkin
authors: OpGen, Inc., Gaithersburg, Maryland, United States of America.
authors: Trevor
authors: T
authors: Wagner
authors: University of Florida, Gainesville, Florida, United States of America.
authors: Chythanya
authors: C
authors: Rajanna
authors: Henry M. Jackson Foundation, Bethesda, Maryland, United States of America; Naval Medical Research Center-Frederick, Fort Detrick, Maryland, United States of America.
authors: Hsinyi
authors: H
authors: Tsang
authors: Genome Science, Biosciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.
authors: Shannon L
authors: SL
authors: Johnson
authors: Naval Medical Research Center-Frederick, Fort Detrick, Maryland, United States of America.
authors: Vishwesh P
authors: VP
authors: Mokashi
authors: Genome Science, Biosciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.
authors: Patrick S G
authors: PS
authors: Chain
authors: Henry M. Jackson Foundation, Bethesda, Maryland, United States of America; Naval Medical Research Center-Frederick, Fort Detrick, Maryland, United States of America.
authors: Shanmuga
authors: S
authors: Sozhamannan
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D002876:Chromosomes, Bacterial / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D016521:Electrophoresis, Gel, Pulsed-Field; D020440:Gene Duplication; D015321:Gene Rearrangement / Q000235:genetics; D014644:Genetic Variation; D059646:Genome Size; D016680:Genome, Bacterial; D054643:INDEL Mutation / Q000235:genetics; D010802:Phylogeny; D015203:Reproducibility of Results; D015183:Restriction Mapping; D017422:Sequence Analysis, DNA; D014734:Vibrio cholerae / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial