SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes

Gulig, Paul A., de Crécy-Lagard, Valerie, Wright, Anita C., Walts, Brandon, Telonis-Scott, Marina and McIntyre, Lauren M. 2010, SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes, BMC Genomics, vol. 11, pp. 1-16, doi: 10.1186/1471-2164-11-512.

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Title SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes
Formatted title SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes
Author(s) Gulig, Paul A.
de Crécy-Lagard, Valerie
Wright, Anita C.
Walts, Brandon
Telonis-Scott, MarinaORCID iD for Telonis-Scott, Marina orcid.org/0000-0002-8524-5538
McIntyre, Lauren M.
Journal name BMC Genomics
Volume number 11
Article ID 152
Start page 1
End page 16
Total pages 16
Publisher BioMed Central
Place of publication London, Eng.
Publication date 2010-09
ISSN 1471-2164
Keyword(s) Animals
Base Sequence
Genes, Bacterial
Genomics
Genotype
Mice
Open Reading Frames
Phenotype
Phylogeny
Plasmids
Polymorphism, Single Nucleotide
Reference Standards
Sequence Analysis, DNA
Vibrio vulnificus
Virulence
Science & Technology
Life Sciences & Biomedicine
Biotechnology & Applied Microbiology
Genetics & Heredity
ENVIRONMENTAL STRAINS
BIOFILM FORMATION
MARINE PATHOGEN
SIALIC-ACID
SHORT-READ
IN-VITRO
CELLS
TECHNOLOGIES
EVOLUTION
Summary BACKGROUND: Vibrio vulnificus is the leading cause of reported death from consumption of seafood in the United States. Despite several decades of research on molecular pathogenesis, much remains to be learned about the mechanisms of virulence of this opportunistic bacterial pathogen. The two complete and annotated genomic DNA sequences of V. vulnificus belong to strains of clade 2, which is the predominant clade among clinical strains. Clade 2 strains generally possess higher virulence potential in animal models of disease compared with clade 1, which predominates among environmental strains. SOLiD sequencing of four V. vulnificus strains representing different clades (1 and 2) and biotypes (1 and 2) was used for comparative genomic analysis. RESULTS: Greater than 4,100,000 bases were sequenced of each strain, yielding approximately 100-fold coverage for each of the four genomes. Although the read lengths of SOLiD genomic sequencing were only 35 nt, we were able to make significant conclusions about the unique and shared sequences among the genomes, including identification of single nucleotide polymorphisms. Comparative analysis of the newly sequenced genomes to the existing reference genomes enabled the identification of 3,459 core V. vulnificus genes shared among all six strains and 80 clade 2-specific genes. We identified 523,161 SNPs among the six genomes. CONCLUSIONS: We were able to glean much information about the genomic content of each strain using next generation sequencing. Flp pili, GGDEF proteins, and genomic island XII were identified as possible virulence factors because of their presence in virulent sequenced strains. Genomic comparisons also point toward the involvement of sialic acid catabolism in pathogenesis.
Language eng
DOI 10.1186/1471-2164-11-512
Field of Research 06 Biological Sciences
11 Medical And Health Sciences
08 Information And Computing Sciences
HERDC Research category C1.1 Refereed article in a scholarly journal
Persistent URL http://hdl.handle.net/10536/DRO/DU:30119543

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