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Title: Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792

Abstract

Vibrio harveyi CAIM 1792 is a marine bacterial strain that causes mortality in farmed shrimp in north-west Mexico, and the identification of virulence genes in this strain is important for understanding its pathogenicity. The goal of this study was to compare the V. harveyi CAIM 1792 genome with related genome sequences to determine their phylogenic relationship and explore unique regions in silico that differentiate this strain from other V. harveyi strains. Twenty-one newly sequenced genomes were compared in silico against the CAIM 1792 genome at nucleotidic and predicted proteome levels. The proteome of CAIM 1792 had higher similarity to those of other V. harveyi strains (78 %) than to those of the other closely related species Vibrio owensii (67 %), Vibrio rotiferianus (63 %) and Vibrio campbellii (59 %). Pan-genome ORFans trees showed the best fit with the accepted phylogeny based on DNA–DNA hybridization and multi-locus sequence analysis of 11 concatenated housekeeping genes. SNP analysis clustered 34/38 genomes within their accepted species. Laslty, the pangenomic and SNP trees showed that V. harveyi is the most conserved of the four species studied and V. campbellii may be divided into at least three subspecies, supported by intergenomic distance analysis. BLASTP atlases weremore » created to identify unique regions among the genomes most related to V. harveyi CAIM 1792; these regions included genes encoding glycosyltransferases, specific type restriction modification systems and a transcriptional regulator, LysR, reported to be involved in virulence, metabolism, quorum sensing and motility.« less

Authors:
 [1];  [2];  [2];  [3];  [1];  [4];  [5];  [1]
  1. CIAD A.C., Mazatlan Unit for Aquaculture, Mazatlan, Sinaloa (Mexico)
  2. Naval Research Lab. (NRL), Washington, DC (United States)
  3. Technical Univ. of Denmark, Lyngby (Denmark)
  4. Technical Univ. of Denmark, Lyngby (Denmark); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  5. Australian Institute of Marine Science, Townsville, Queensland (Australia)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1302917
DOE Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Microbiology
Additional Journal Information:
Journal Volume: 161; Journal Issue: 9; Journal ID: ISSN 1350-0872
Publisher:
Microbiology Society
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

Espinoza-Valles, Iliana, Vora, Gary J., Lin, Baochuan, Leekitcharoenphon, Pimlapas, González-Castillo, Adrián, Ussery, David W., Høj, Lone, and Gomez-Gil, Bruno. Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792. United States: N. p., 2015. Web. doi:10.1099/mic.0.000141.
Espinoza-Valles, Iliana, Vora, Gary J., Lin, Baochuan, Leekitcharoenphon, Pimlapas, González-Castillo, Adrián, Ussery, David W., Høj, Lone, & Gomez-Gil, Bruno. Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792. United States. doi:10.1099/mic.0.000141.
Espinoza-Valles, Iliana, Vora, Gary J., Lin, Baochuan, Leekitcharoenphon, Pimlapas, González-Castillo, Adrián, Ussery, David W., Høj, Lone, and Gomez-Gil, Bruno. Fri . "Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792". United States. doi:10.1099/mic.0.000141.
@article{osti_1302917,
title = {Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792},
author = {Espinoza-Valles, Iliana and Vora, Gary J. and Lin, Baochuan and Leekitcharoenphon, Pimlapas and González-Castillo, Adrián and Ussery, David W. and Høj, Lone and Gomez-Gil, Bruno},
abstractNote = {Vibrio harveyi CAIM 1792 is a marine bacterial strain that causes mortality in farmed shrimp in north-west Mexico, and the identification of virulence genes in this strain is important for understanding its pathogenicity. The goal of this study was to compare the V. harveyi CAIM 1792 genome with related genome sequences to determine their phylogenic relationship and explore unique regions in silico that differentiate this strain from other V. harveyi strains. Twenty-one newly sequenced genomes were compared in silico against the CAIM 1792 genome at nucleotidic and predicted proteome levels. The proteome of CAIM 1792 had higher similarity to those of other V. harveyi strains (78 %) than to those of the other closely related species Vibrio owensii (67 %), Vibrio rotiferianus (63 %) and Vibrio campbellii (59 %). Pan-genome ORFans trees showed the best fit with the accepted phylogeny based on DNA–DNA hybridization and multi-locus sequence analysis of 11 concatenated housekeeping genes. SNP analysis clustered 34/38 genomes within their accepted species. Laslty, the pangenomic and SNP trees showed that V. harveyi is the most conserved of the four species studied and V. campbellii may be divided into at least three subspecies, supported by intergenomic distance analysis. BLASTP atlases were created to identify unique regions among the genomes most related to V. harveyi CAIM 1792; these regions included genes encoding glycosyltransferases, specific type restriction modification systems and a transcriptional regulator, LysR, reported to be involved in virulence, metabolism, quorum sensing and motility.},
doi = {10.1099/mic.0.000141},
journal = {Microbiology},
issn = {1350-0872},
number = 9,
volume = 161,
place = {United States},
year = {2015},
month = {1}
}

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