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 aim of this work 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. 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.
authors.affiliation: CIAD A.C., Mazatlán Unit for Aquaculture, Mazatlán, Sinaloa, Mexico.
authors.forename: Iliana
authors.initials: I
authors.lastname: Espinoza-Valles
authors.affiliation: Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA.
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Vora
authors.affiliation: Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA.
authors.forename: Baochuan
authors.initials: B
authors.lastname: Lin
authors.affiliation: National Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kongens Lyngby, Denmark.|Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Pimlapas
authors.initials: P
authors.lastname: Leekitcharoenphon
authors.affiliation: CIAD A.C., Mazatlán Unit for Aquaculture, Mazatlán, Sinaloa, Mexico.
authors.forename: Adrián
authors.initials: A
authors.lastname: González-Castillo
authors.affiliation: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.|Comparative Genomics group, Biosciences Division, Oak Ridge National Labs, Oak Ridge, Tennessee, USA.
authors.forename: Dave
authors.initials: D
authors.lastname: Ussery
authors.affiliation: Australian Institute of Marine Science, Townsville, Queensland, Australia.
authors.forename: Lone
authors.initials: L
authors.lastname: Høj
authors.affiliation: CIAD A.C., Mazatlán Unit for Aquaculture, Mazatlán, Sinaloa, Mexico.
authors.forename: Bruno
authors.initials: B
authors.lastname: Gomez-Gil
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D017124:Conserved Sequence; D033364:Decapoda / Q000382:microbiology; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D005810:Multigene Family; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D020543:Proteome; D014733:Vibrio / Q000145:classification / Q000235:genetics* / Q000378:metabolism
chemical_list: D020543:Proteome