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Table 4 Genome comparison of Chilean pandemic V. parahaemolyticus isolates

From: Genome diversification within a clonal population of pandemic Vibrio parahaemolyticus seems to depend on the life circumstances of each individual bacteria

Segment

Properties

ATC 220

PMC 14.7

PMC 48

PMA 37.5

PMC 58.5

PMA 109.5

PMC 58.7

ATC 210

 

Regions formed by reads unaligned with RIMD 2210633

        

5,665 bp Insert

Insertion Sequence in position 674,415 of RIMD 2210633. Similarity with phage integrase and mobile element protein found in V. parahaemolyticus UCM-V493 [21]. GC% = 36.7. Average GC% in RIMD 2210633 is 45.4%

-

P

P

P

P

P

P

P

6,637 bp Insert

6,637 bp inserted in position 2.803.591 of RIMD 2210633. Closely related with regions found in other Vibrio species. With segments assigned to CDS designated as phage integrase and putative transposase. GC% = 41.5

-

-

-

P

-

-

-

-

160/384 bp Inserts

5 to 12 tandem repeats with 32 bp units potentially inserted in two isolates at different positions. GC% = 50.0

-

-

-

P

-

-

P

P

Prophage VP58.5

Lineal plasmid prophage of temperate bacteriophage VP58.5 [14,15]. GC% = 50.9

-

-

-

-

P

P

-

-

82.0 Kb plasmid

83% coverage with 80% identity to plasmid p0908, a putative prophage also found in a Vibrio sp. [23]. GC% = 45.1

-

-

-

-

-

P

-

-

85.8 Kb plasmid

97% coverage with 99% identity to plasmid pVPUCMV of environmental strain V. parahaemolyticus UCM- V493 [21]. It might be a prophage but only a few ORFs are annotated. GC% = 40.8

-

-

-

-

-

P

-

-

361 bp contig

327 bp 91% identity pvdJ in drug resistant Ps. Aeruginosa PA381812. GC% = 49.0

-

-

-

P

-

-

-

-

 

Regions in RIMD 2210633 not covered by reads from at least one other isolate

        

Chromosome 1*

         

396,525–396,578

16/93 bp without annotation in reference genome

-

-

P

P

P

-

P

P

670,436–670,451

16 bp VP0639 Hypothetical

P

P

P

P

P

P

P

-

671,192–671,222

31 bp without annotation in reference genome

P

P

P

P

P

P

P

-

1,658,835–1,667,479

8644 bp in PMC48 corresponding to VP1575-VP1583, genes of prophage f237

P

P

-

P

P

P

P

P

1,674,168–1,677,729

2.042 bp in ATC210 corresponding to VP1575-VP1583, genes of prophage alpha

P

P

P

P

P

P

P

-

2,214,140–2,214,156

Not annotated in RIMD 2210633.

P

P

P

-

P

P

P

P

2,301,625–2,301,708

27 bp in VP2191

P

P

P

-

P

P

P

P

2,697,003–2,698,067

1064 bp in VP2552, DNA mismatch repair protein MutS

P

P

P

P

P

P

-

P

Chromosome 2*

         

991,612–991,642

8-31 bp VPA0953 biofilm-associated surface protein

P

P

P

-

P

P

P

-

  1. *Positions indicated in column Segment correspond to the larger uncovered segment.
  2. P: Presence of the segment.
  3. Presence and properties of regions not present in every Chilean isolate’s genome.