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

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

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

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].
^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.
^b ymf65, ymf66, ymf67 and ymf76 each appear to be equivalent to two adjacent ORFs in P. tetraurelia. Comparative data are omitted.
^c ymf87 was only found in P. caudatum
^d rps19 in P. tetraurelia was annotated during the present work

ISSN: 1471-2164