title: Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade.
abstract: The core of the Vibrio Harveyi clade contains V. harveyi, V. campbellii, V. owensii, V. jasicida, and V. rotiferianus. They are well recognized aquatic animal pathogens, but misclassification has been common due to similarities in their rDNA sequences and phenotypes. To better understand their evolutionary relationships and functional features, we sequenced a shrimp pathogen strain V. harveyi 1114GL, reclassified it as V. campbellii and compared this and 47 other sequenced Vibrio genomes in the Harveryi clade. A phylogeny based on 1,775 genes revealed that both V. owensii and V. jasicida were closer to V. campbellii than to V. harveyi and that V. campbellii strains can be divided into two distinct groups. Species-specific genes such as intimin and iron acquisition genes were identified in V. campbellii. In particular, the 1114GL strain contains two bacterial immunoglobulin-like genes for cell adhesion with 22 Big_2 domains that have been extensively reshuffled and are by far the most expanded among all species surveyed in this study. The 1114GL strain differed from ATCC BAA-1116 by ~9% at the synonymous sites, indicating high diversity within V. campbellii. Our study revealed the characteristics of V. campbellii in the Harveyi clade and the genetic basis for their wide-spread pathogenicity.
authors.affiliation: Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.|Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Huei-Mien
authors.initials: HM
authors.lastname: Ke
authors.affiliation: Centex Shrimp, Faculty of Science, Mahidol University, Bangkok, Thailand.|Shrimp-Virus Interaction Laboratory, Animal Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
authors.forename: Anuphap
authors.initials: A
authors.lastname: Prachumwat
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Chun-Ping
authors.initials: CP
authors.lastname: Yu
authors.affiliation: Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.|Department of Life Science, National Taiwan University, Taipei, Taiwan.
authors.forename: Yi-Ting
authors.initials: YT
authors.lastname: Yang
authors.affiliation: Centex Shrimp, Faculty of Science, Mahidol University, Bangkok, Thailand.|Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand.
authors.forename: Sutitcha
authors.initials: S
authors.lastname: Promsri
authors.affiliation: Tungkang Biotechnology Research Center, Fisheries Research Institute, Council of Agriculture, Pingtung, Taiwan.
authors.forename: Kuan-Fu
authors.initials: KF
authors.lastname: Liu
authors.affiliation: Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.|Department of Life Science, National Taiwan University, Taipei, Taiwan.|Center of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Chu-Fang
authors.initials: CF
authors.lastname: Lo
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Mei-Yeh Jade
authors.initials: MJ
authors.lastname: Lu
authors.affiliation: Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.|Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.|Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
authors.forename: Mei-Chin
authors.initials: MC
authors.lastname: Lai
authors.affiliation: Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.|Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Isheng J
authors.initials: IJ
authors.lastname: Tsai
authors.affiliation: Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.|Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.|Department of Ecology and Evolution, University of Chicago, Chicago, US.
authors.forename: Wen-Hsiung
authors.initials: WH
authors.lastname: Li
mesh_terms: D001483:Base Sequence; D004251:DNA Transposable Elements / Q000235:genetics; D018628:Gene Dosage; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D010802:Phylogeny; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D026801:Synteny / Q000235:genetics; D014733:Vibrio / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements