Skip to main content

Table 2 Orthologous genes with evidence of homologous recombination detected by both PHI and RDP4

From: Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica

Gene

No. of taxaa

Functionb

Serotype-associatedc

PHI p value

RDPd

GENECONVd

Bootscand

Maxchid

Chimaerad

SiSscand

3Seqd

Cluster_25

90

oxidoreductase FeS-binding subunit

N

0.004813

   

3.74E-03

2.87E-02

4.17E-08

0.03547

Cluster_32

90

MFS transporter

N

< 0.0005

2.75E-05

 

3.02E-02

6.11E-10

 

2.20E-22

3.23E-07

Cluster_52

64

phage tail protein

N

< 0.0005

7.38E-17

5.85E-18

3.99E-18

6.09E-12

9.23E-13

3.88E-15

2.81E-24

Cluster_3844

64

phage tail protein

N

< 0.0005

9.42E-10

3.59E-07

2.92E-06

1.13E-11

3.03E-13

1.04E-15

7.99E-18

Cluster_3925

70

phage tail protein

N

0.004785

2.93E-03

  

5.82E-10

3.01E-07

3.85E-23

7.85E-05

Cluster_4291

57

phage tail protein I

Y

< 0.0005

  

3.10E-03

2.07E-07

3.77E-05

 

3.30E-05

Cluster_4292

57

recombinase

Y

0.01689

4.56E-03

8.03E-03

4.72E-03

6.89E-06

1.32E-06

1.01E-04

2.34E-06

Cluster_4306

52

mercuric transport protein periplasmic component

N

0.007786

 

1.51E-08

 

6.83E-05

8.67E-04

 

3.06E-03

Cluster_4307

52

mercuric transport protein

N

0.002263

3.91E-07

7.08E-06

2.05E-07

5.77E-05

2.23E-04

1.57E-09

1.01E-06

Cluster_4308

53

portal protein

Y

< 0.0005

2.37E-14

9.40E-09

2.38E-14

3.37E-14

  

2.66E-27

Cluster_4309

53

hypothetical protein

Y

< 0.0005

1.72E-05

2.65E-03

 

1.63E-12

9.43E-08

 

4.90E-06

Cluster_4310

53

DNA transfer protein

Y

0.002031

1.30E-03

7.12E-04

 

6.10E-08

2.54E-04

4.43E-05

1.73E-04

Cluster_4343

53

RecBCD nuclease inhibitor

Y

< 0.0005

3.10E-05

2.10E-05

3.09E-06

4.82E-08

2.58E-06

1.16E-08

1.51E-06

Cluster_4344

53

recombinase

Y

< 0.0005

 

1.05E-02

 

3.44E-02

2.66E-02

 

2.01E-04

Cluster_4345

53

hypothetical protein

Y

< 0.0005

 

5.39E-04

5.88E-04

3.18E-07

2.55E-03

2.45E-09

4.45E-03

Cluster_4355

52

phage tail protein

Y

< 0.0005

1.13E-09

7.64E-04

2.42E-06

3.57E-11

1.02E-03

 

3.51E-02

Cluster_4361

48

peptidase

Y

< 0.0005

3.81E-09

 

3.92E-12

4.40E-04

3.19E-05

 

1.13E-07

Cluster_4432

48

terminase

Y

< 0.0005

2.89E-11

3.68E-10

2.02E-09

1.67E-17

7.22E-08

1.55E-42

4.83E-46

Cluster_4484

49

endonuclease

Y

< 0.0005

1.81E-17

2.25E-18

3.38E-14

2.63E-03

1.42E-03

8.97E-35

1.08E-36

Cluster_4488

40

phage tail tape measure protein

Y

< 0.0005

2.99E-02

3.41E-03

1.81E-04

1.26E-04

6.51E-03

2.38E-17

1.73E-12

Cluster_4533

47

phage portal protein

Y

< 0.0005

2.78E-10

6.75E-10

5.49E-09

5.22E-10

7.45E-04

9.57E-18

9.99E-18

Cluster_4534

47

capsid protein

Y

0.01974

   

9.04E-09

3.53E-03

4.91E-09

2.78E-03

Cluster_4543

47

baseplate assembly protein

Y

< 0.0005

2.80E-07

6.92E-18

4.96E-03

3.08E-19

5.29E-09

5.49E-03

1.26E-23

Cluster_4548

47

phage tail tape measure protein

Y

0.01543

   

3.98E-03

3.09E-03

4.16E-04

1.25E-02

Cluster_4549

47

phage tail protein

Y

0.008323

3.81E-84

3.34E-76

4.42E-76

9.86E-40

1.45E-41

6.19E-30

4.44E-16

Cluster_4562

46

acyltransferase

Y

< 0.0005

 

1.26E-06

3.40E-09

8.88E-09

4.05E-05

1.26E-11

4.13E-06

Cluster_4594

44

coat protein

Y

< 0.0005

 

8.20E-94

2.62E-96

2.28E-24

1.67E-24

3.81E-31

2.22E-15

Cluster_4595

44

endorhamnosidase

Y

< 0.0005

5.09E-12

2.93E-10

6.52E-12

4.87E-11

4.76E-12

5.27E-11

7.77E-15

Cluster_4658

31

hypothetical protein

Y

< 0.0005

2.26E-06

2.30E-03

 

5.76E-04

1.95E-03

 

9.80E-04

Cluster_4805

37

DNA-invertase

N

< 0.0005

2.98E-41

3.16E-35

5.25E-38

8.71E-15

2.73E-11

1.33E-12

8.88E-16

Cluster_4879

31

DNA transfer protein

Y

0.001663

8.93E-11

2.59E-05

2.43E-06

2.58E-13

2.32E-02

2.16E-09

1.82E-04

Cluster_5031

31

protein NinG

Y

< 0.0005

2.85E-08

3.32E-09

 

8.24E-08

4.16E-08

1.95E-10

1.21E-09

Cluster_5479

19

resolvase

Y

< 0.0005

3.90E-09

8.64E-07

4.57E-08

5.37E-10

9.25E-09

9.55E-07

6.43E-13

Cluster_5556

17

replication of DNA

Y

< 0.0005

 

6.88E-30

1.04E-43

9.83E-28

 

4.13E-29

7.14E-79

Cluster_5572

16

DNA methylase

Y

< 0.0005

4.00E-03

1.32E-03

 

9.25E-04

7.54E-05

3.24E-05

1.52E-03

Cluster_5598

15

methyltransferase

Y

0.00691

1.70E-02

 

5.20E-03

2.55E-05

  

6.62E-05

Cluster_5601

15

relaxase NikB

Y

< 0.0005

1.36E-08

3.65E-05

1.39E-08

9.80E-10

  

2.41E-15

Cluster_5602

15

conjugal transfer protein TrbC

Y

0.02477

  

6.49E-03

3.23E-04

4.18E-03

 

2.77E-02

Cluster_5607

15

hypothetical protein

Y

< 0.0005

3.06E-19

8.34E-20

3.60E-21

1.58E-17

2.82E-19

7.02E-17

1.11E-15

Cluster_5609

15

conjugal transfer protein

Y

< 0.0005

 

1.98E-02

6.21E-04

2.37E-04

  

1.92E-05

Cluster_5640

15

hypothetical protein

Y

0.005552

3.33E-02

5.88E-03

3.31E-04

1.36E-02

6.51E-03

1.18E-04

5.09E-04

Cluster_6042

5

oxaloacetate decarboxylase

N

< 0.0005

 

6.88E-03

2.66E-02

9.52E-05

  

1.27E-07

  1. aNumber of isolates with the corresponding cluster gene
  2. bFunction was determined by NCBI Prokaryotic Genome Annotation Pipeline
  3. cY: serotype-clustered core genes (i.e., showed clustering by serotype in the gene tree), or serotype-associated accessory genes (i.e., significantly over- or under- represented in one serotype)
  4. N not serotype-clustered core genes nor serotype-associated accessory genes
  5. dp value of the statistic test; only significant p-values (< 0.05) are shown