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Table 3 De novo genes

From: Gene gain and loss events in Rickettsia and Orientiaspecies

 

Gene (sequence length *)

Found in

Size (nt)

Ka/Ks

P-value

Coding region

AT %

1

raf_ORF0703 (335 nt)

R. conorii

336

0.257

0.0357

 

57.6%

  

R. rickettsii

477

1.628

0.046

Yes

 

2

raf_ORF0265 (389 nt)

R. conorii

390

0.84

0.0233

Yes

49.6%

3

raf_ORF0391

(428 nt)

R. felis

351

1.5352

0.3244

No

51.1%

4

raf_ORF0649 (449 nt)

R. massiliae

309

1.355

0.1443

 

61.4%

  

R. felis

363

1.794

0.7871

  
  

R. bellii

432

1.568

0.4576

No

 

5

raf_ORF1011 (551 nt)

R. felis

555

1.239

0.9519

No

62.7%

6

raf_ORF1025 (311 nt)

R. felis

309

0.879

0.7758

No

63%

7

raf_ORF0586 (347 nt)

R. conorii

348

1.257

0.0719

 

58.2%

  

R. akari

147

2.171

0.6816

No

 

8

raf_ORF0724 (569 nt)

R. rickettsii

354

0.154

0.1146

 

58.8%

  

R bellii

585

1.45

0.6896

No

 

9

raf_ORF0390 (1001 nt)

R. massiliae

432

1.479

0.0888

 

55.3%

  

R. rickettsii

579

0.639

0.1011

  
  

R. felis

744

0.649

0.7778

  
  

R. bellii

834

0.555

0.152

No

 

10

raf_ORF0053 (488 nt)

R. conorii

474

0.615

0.1924

 

59%

  

R. massiliae

489

0.579

0.2145

  
  

R. rickettsii

489

0.561

0.2427

  
  

R. felis

489

0.674

0.2498

  
  

R. akari

489

0.713

0.4433

No

 

11

raf_ORF0348 (593 nt)

R. conorii

594

1.427

0.0494

Yes

58%

  

R. massiliae

378

1.123

0.3122

  
  

R. rickettsii

405

0.492

0.0917

  
  

R. felis

603

1.517

0.9648

  
  

R. akari

576

1.076

0.3832

No

 

12

raf_ORF0876 (378 nt)

R. felis

486

0.921

0.2213

 

51%

  

R. bellii

486

1.354

0.636

No

 

13

raf_ORF0172 (1169 nt)

R. conorii

1158

0.773

0.0564

 

52.8%

  

R. massiliae

1170

0.764

0.0989

  
  

R. rickettsii

1185

0.069

0.2337

No

 

14

raf_ORF0993 (320 nt)

R. massiliae

321

0.942

0.059

 

57%

  

R. typhi

435

0.1905

0.544

No

 

15

raf_ORF0046 (520 nt)

R. conorii

519

0.406

0.0174

Yes

58%

  

R. massiliae

408

1.53

0.0684

No

 
  

R. akari

483

0.977

0.3574

No

 

16

raf_ORF0275 (1394 nt)

R. conorii

1395

1.83

0.0262

Yes

55.6%

  

R. massiliae

1404

1.084

0.0614

No

 
  

R. rickettsii

1395

0.767

0.0348

Yes

 
  

R. felis

1395

0.9

0.1505

  
  

R. akari

1422

0.873

0.2144

  
  

R. canadensis

1389

1.133

0.344

No

 

17

raf_ORF0921 (647 nt)

R. conorii

576

0.62

0.0365

Yes

57.4%

  

R. felis

645

0.642

0.2394

No

 
  1. When the ω ratio was significantly inferior to 1 (p-value < 0.05), we considered that we have a coding region. According to the ω ratio test, raf_ORF0703 and raf_ORF0265 are functional.
  2. Their function in not known. On the contrary, the twelve following sequences seem to correspond to no coding regions, while raf_ORF0046, raf_ORF0275 and raf_ORF0921 seem to be non-functional. Only a transcriptomic analysis could show for sure if these regions are really coding or not. By chance, all of these genes are found in R. africae and to calculate the ω ratio we took as reference sequence the R. africae sequence.
  3. * The length given in nucleotides is the sequence length in Rickettsia africae and the AT % content is the one corresponding to Rickettsia africae.
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