Research article
Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus
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* Corresponding author: E Fidelma Boyd fboyd@udel.edu
1 Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
2 Department of Microbiology, UCC, National University of Ireland-Cork, Ireland
3 Center for Biological Sequence Analysis, BioCentrum, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
4 Department of Epidemiology and Preventive Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
5 Department of Medical Technology, University of Delaware, Newark, DE 19716, USA
BMC Microbiology 2008, 8:110 doi:10.1186/1471-2180-8-110
Published: 30 June 2008Additional files
Additional file 1:
Fig. S1. Genome BLAST Atlas of V. parahaemolyticus RIMD2210633 as reference strain (inner most circle) versus 27 genomes of members of the family Vibrionaceae for chromosome 1. V. parahaemolyticus RIMD2210633 as reference strain (inner most circle) versus V. parahaemolyticus AQ3810, V. cholerae 1587, AM-19226, MAK757, MO10, MZO-2, MZO-3, B33, NCTC8457, RC385, O395, V51, V52, 623-39, and 2740-80, V. harveyi ATCCBAA116, V. alginolyticus 12G01, Vibrio sp. Ex25, V. vulnificus CMCP6 and YJ016, V. splendidus 12B01, Vibrio sp. MED222, V. fischeri ES114, V. salmonicida LF1238, V. angustum S14, P. profundum SS9 and 3TCK for chromosome 1. The gaps or holes in the outer four circles represent regions present in V. parahaemolyticus strain RIMD2210633 that are absent from the other species. The innermost circles show DNA structure features, DNA stacking energy, DNA position preference, positive and negative coding strands are indicated by dark blue and red circle. Global direct and global inverted repeats are represented and the two inner most circles represent GC shew and AT content, respectively.
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Additional file 2:
Fig. S2. Genome BLAST Atlas of V. parahaemolyticus RIMD2210633 as reference strain (inner most circle) versus 27 genomes of members of the family Vibrionaceae for chromosome 2. V. parahaemolyticus RIMD2210633 as reference strain (inner most circle) versus V. parahaemolyticus AQ3810, V. cholerae 1587, AM-19226, MAK757, MO10, MZO-2, MZO-3, B33, NCTC8457, RC385, O395, V51, V52, 623-39, and 2740-80, V. harveyi ATCCBAA116, V. alginolyticus 12G01, Vibrio sp. Ex25, V. vulnificus CMCP6 and YJ016, V. splendidus 12B01, Vibrio sp. MED222, V. fischeri ES114, V. salmonicida LF1238, V. angustum S14, P. profundum SS9 and 3TCK for chromosome 2. The gaps or holes in the outer four circles represent regions present in V. parahaemolyticus strain RIMD2210633 that are absent from the other species. The innermost circles show DNA structure features, DNA stacking energy, DNA position preference, positive and negative coding strands are indicated by dark blue and red circle. Global direct and global inverted repeats are represented and the two inner most circles represent GC shew and AT content, respectively.
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Additional file 3:
Fig. S3. Linear comparison of V. parahaemolyticus RIMD2210633 and AQ3810 created using ACT (Artemis Comparison Tool) at the insertion sites of (A) VPaI-1 and VPaI-4, and (B) VPaI-5 and VPaI-6. A homologous block of genomic sequence (BLASTN matches) is indicated by red lines between the chromosomal regions examined. The location of the genomic islands (GIs) identified in RIMD2210633 are illustrated above, and in AQ3810 below the genome comparison. Horizontal arrows represent annotated genes, striped arrows represent integrases, and the direction of the arrow indicates gene orientation.
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Additional file 4:
Fig. S4. Linear comparison of V. parahaemolyticus strain RIMD2210633 and strain AQ3810 created using ACT [59] at the insertion sites of (A) VPaI-2 and VPaI-3, and (B) VPaI-9 and VPaI-10. A homologous block of genomic sequence (BLASTN matches) is indicated by red and blue lines between the chromosomes; blue lines indicate chromosomal inversion events. The location of Vibrio parahaemolyticus islands (VPaIs) identified is illustrated above for RIMD2210633 and below for AQ3810 the region examined. Horizontal arrows represent annotated genes, striped arrows represent integrases, and the direction of the arrow indicates gene orientation.
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Additional file 5:
Table S1. PCR assays of the distribution of 11 regions unique to V. parahaemolyticus.
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