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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.