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Table 1 Gene phylogenies for OriI and OriII.

From: Vibrio chromosomes share common history

 

Relation to hypothesized chromosome phylogeny

Sequence set

Resolution

V. alginolyticus/V. parahaemolyticus clade

 

Consistent (A)

Conditionally consistent (B)

Uninformative (U)

Inconsistent (I)

Complete(C)

Incomplete (P)

Full (F)

Partial (N)

Unresolved (U)

Consistent with consensus(-)

Scrambled (X)

Other issues (see text) (O)

Tree uninformative (n/a)

C1

    

LysR

A

P

N

-

MDR

A

P

F

-

UDP

I

C

N

-

Epsilon

B

C

N

O

Beta

B

C

N

O

Gamma

B

P

N

-

Alpha

A

C

N

-

Delta

A

C

N

X

Bsub

A

C

N

-

Csub

U

C

U

n/a

Asub

I

C

N

-

Isub

A

C

N

X

ParB

A

C

N

-

ParA

A

C

N

-

GidB

A

C

N

-

GidA

B

C

N

-

MioC

B

C

F

X

ThdF

B

C

N

X

YidC

A

C

N

X

RnpA

A

C

N

-

RpmH

U

P

U

n/a

ABC1

A

P

N

X

ABC2

A

P

N

-

ABC3

A

P

N

-

DnaA

A

C

N

-

DnaN

A

C

N

-

RecF

B

C

F

X

GyrB

B

C

F

-

C2

    

MetC

A

P

F

X

GluP

B

P

N

X

PyrD

A

P

N

-

GTP

A

P

F

-

Hyp

A

P

N

-

TraR

A

P

N

-

RctB

A

C

N

-

ParA2

A

C

N

-

ParB2

A

C

N

-

ChrR

A

C

N

X

Poly

B

P

F

-

Chlor

A

P

F

-

  1. All the genes analyzed are listed. The first column represents whether the estimated phylogeny was consistent with the hypothesized chromosome phylogeny (A and B, if removing cholera results in a consistent tree), inconsistent with the hypothesized phylogeny, or simply uninformative. The second column indicates whether all strains were represented for this locus and the third whether there were any clades outside the cholera clade at which the tree was a polytomy because of an uninformative or unsupported node. The fourth column includes cases in which V. splendidus is out of place in the tree (O) or where the V. parahaemolyticus/V. alginolyticus clade is not the same as in the consensus tree (X).
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BMC Microbiology

ISSN: 1471-2180

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