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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