Title : Genomic taxonomy of Vibrios - Thompson_2009_BMC.Evol.Biol_9_258
Author(s) : Thompson CC , Vicente AC , Souza RC , Vasconcelos AT , Vesth T , Alves N, Jr. , Ussery DW , Iida T , Thompson FL
Ref : BMC Evol Biol , 9 :258 , 2009
Abstract :

BACKGROUND: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. RESULTS: We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, < or = 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. CONCLUSION: The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding.

PubMedSearch : Thompson_2009_BMC.Evol.Biol_9_258
PubMedID: 19860885
Gene_locus related to this paper: vibal-q1v7b5 , vibal-q1v7d0 , vibal-q1v463 , vibal-q1v627 , vibal-q1v697 , vibal-q1va42 , vibal-q1vai8 , vibal-q1vap1 , vibal-q1vbx2 , vibal-q1vfw6 , vibch-a6xrz3 , vibch-VC2718 , vibch-VCA0688 , vibch-y1892 , vibch-y2276 , vibha-d0x5c8 , vibha-d0x7p9 , vibha-d0xb11 , vibha-d0xgc5 , vibcb-a7mwv0 , vibhb-a7mzs1 , vibhb-a7n5i4 , vibhb-bioh , vibmi-d2y908 , vibmi-d2ygk2 , vibpa-PHAC , vibpa-VPA0468 , vibpa-VPA1467 , vibpa-VPA1496 , vibpa-VPA1595 , vibal-d0wu09 , vibha-d0xda8 , vibmi-u4zh77 , 9vibr-k5u9q4 , vibmi-g0sil5

Related information

Gene_locus vibal-q1v7b5    vibal-q1v7d0    vibal-q1v463    vibal-q1v627    vibal-q1v697    vibal-q1va42    vibal-q1vai8    vibal-q1vap1    vibal-q1vbx2    vibal-q1vfw6    vibch-a6xrz3    vibch-VC2718    vibch-VCA0688    vibch-y1892    vibch-y2276    vibha-d0x5c8    vibha-d0x7p9    vibha-d0xb11    vibha-d0xgc5    vibcb-a7mwv0    vibhb-a7mzs1    vibhb-a7n5i4    vibhb-bioh    vibmi-d2y908    vibmi-d2ygk2    vibpa-PHAC    vibpa-VPA0468    vibpa-VPA1467    vibpa-VPA1496    vibpa-VPA1595    vibal-d0wu09    vibha-d0xda8    vibmi-u4zh77    9vibr-k5u9q4    vibmi-g0sil5
Gene_locus_frgt vibal-q1vca8

Citations formats

Thompson CC, Vicente AC, Souza RC, Vasconcelos AT, Vesth T, Alves N, Jr., Ussery DW, Iida T, Thompson FL (2009)
Genomic taxonomy of Vibrios
BMC Evol Biol 9 :258

Thompson CC, Vicente AC, Souza RC, Vasconcelos AT, Vesth T, Alves N, Jr., Ussery DW, Iida T, Thompson FL (2009)
BMC Evol Biol 9 :258