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Table 1 Size of protein-coding genes in P. caudatum mtDNA and comparative data calculated for P. caudatum and P. tetraurelia

From: The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium

gene length (in aa) sequence identity Ka/Ks ORF length (in aa) sequence identity Ka/Ks
cob 442 0.91 0.012 ymf56 81 0.73 0.067
cox1 745 0.93 0.019 ymf57 105 0.77 0.069
cox2 577 0.84 0.022 ymf59 127 0.40 0.340
atp9 75 1.00 0.001 ymf61 189 0.40 0.298
yejR a 447 0.47 0.242 ymf63 a 525 0.44 0.258
nad1_a 287 0.93 0.012 ymf64 a 1712 0.56 0.168
nad1_b 63 0.71 0.027 ymf65 b 365 - -
nad2 167 0.67 0.093 ymf66 b 412 - -
nad3 120 0.83 0.033 ymf67 b 354 - -
nad4 501 0.70 0.062 ymf68 395 0.76 0.044
nad4L 115 0.64 0.070 ymf76 b 399 - -
nad5 597 0.75 0.049 ymf78 69 0.48 0.298
nad6 256 0.73 0.064 ymf79 73 0.38 0.323
nad7 423 0.91 0.010 ymf80 97 0.68 0.076
nad9 184 0.67 0.072 ymf83 168 0.55 0.206
nad10 154 0.95 0.006 ymf84 158 0.33 0.291
rps3 a 363 0.57 0.195 ymf87 c 107 - -
rps12 139 0.84 0.024     
rps13 244 0.66 0.049     
rps14 102 0.59 0.104     
rps19 d 88 0.46 0.188     
rpl2 265 0.68 0.523     
rpl6 178 0.71 0.055     
rpl14 119 0.75 0.030     
rpl16 166 0.74 0.047     
  1. The sequence identity values were calculated from amino acid sequences. The Ka/Ks ratio was estimated using the method of Goldman and Yang [47] as implemented in the program Ka/Ks_Calculator [28].
  2. a yejR, rps3, ymf63 and ymf64 were considerably longer in the mtDNA of P. caudatum. For comparative analyses the sequences were adjusted to the gene length in P. tetraurelia.
  3. b ymf65, ymf66, ymf67 and ymf76 each appear to be equivalent to two adjacent ORFs in P. tetraurelia. Comparative data are omitted.
  4. c ymf87 was only found in P. caudatum
  5. d rps19 in P. tetraurelia was annotated during the present work