Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

Minxiao, Wang; Song, Sun; Chaolun, Li; Xin, Shen

doi:10.1186/1471-2164-12-73

Table 1 Mitochondrial genome profile and nucleotide composition of C. sinicu s.

From: Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

Feature	strand	Position	Length	Start	Stop	AT %	GC-skew	AT-skew	intergenic nt²
*rrnL* ³	H	2244 - 3382	1139			71.7	0.0567	0.0126	>2959(LNR1)
*trnV*	H	3383 - 3447	65			83.1	-0.0888	0.0734	3
*trnD*	H	3457 - 3518	62			80.6	0.165	0.000	9
*trnT*	H	3531 - 3593	63			74.6	-0.126	-0.0643	12
*trnS2*	L	3594 - 3650	57			73.7	0.202	0.0475	0
*cox1*	L	3660 - 5207	1548	ATA	TAA	59.0	0.0439	-0.190	9
*nad4L*	H	5336 - 5671	336	ATA	TAG	61.9	0.0919	-0.202	128(LNR2)
*cytb*	L	5751 - 6887	1137	ATG	TAA	60.2	-0.0050	-0.249	79
*nad6*	L	6898 - 7377	480	ATT	TAG	62.3	0.0822	-0.149	10
*rrnS* ³	L	7429 - 8082	654			73.1	0.264	0.0369	51
*trnG*	L	8083 - 8146	64			87.6	0.000	0.000	3
*nad1*	L	8147 - 9063	917	ATA	TA¹	62.5	0.000	-0.174	0
*trnF*	L	9064 - 9126	63			66.6	0.237	0.000	0
*trnI*	L	9131 - 9193	63			58.7	0.153	0.0801	4
*nad5*	H	9231 - 10954	1724	ATT	TA¹	59.5	0.0272	-0.109	37
*trnH*	H	10955 - 11017	63			69.8	0.369	0.0917	0
*trnA*	H	12788 - 12851	64			67.2	0.0488	-0.164	1770(LNR3)
*trnY*	H	12852 - 12912	61			60.6	0.000	-0.0264	0
*trnE*	L	12908 - 12971	64			68.7	0.000	0.0451	-5
*trnQ*	L	13002 - 13067	66			77.5	0.604	-0.102	30
*trnL1*	L	13080 - 13143	64			80.1	0.431	0.104	12
*trnP*	L	13178 - 13240	63			76.2	0.202	-0.0420	34
*trnM*	L	13246 - 13309	64			68.7	-0.0990	0.0917	5
*trnK*	L	13312 - 13374	63			68.2	-0.101	0.0235	2
*trnW*	L	13376 - 13439	64			78.1	-0.142	0.0807	1
*trnS1*	L	13439 - 13498	60			77.0	-0.144	-0.0208	-1
*trnN*	L	13498 - 13565	68			61.8	-0.154	0.0485	-1
*cox2*	L	13571 - 14275	705	ATT	TAA	62.6	0.0749	-0.166	5
*nad3*	H	14338 - 14691	354	ATT	TAA	61.3	0.183	-0.318	62
*cox3*	L	14794 - 15585	792	ATG	TAA	57.1	0.0536	-0.208	102(LNR4)
*nad4*	H	16357 - 17658	1302	ATA	TAA	59.9	-0.0697	-0.142	771(LNR5)
*trnL2*	H	17663 - 17728	66			69.7	0.102	0.174	4
*nad2*	H	17729 - 18697	969	ATA	TAA	61.9	-0.0761	-0.202	0
*atp8*	H	18870 - 19031	162	ATT	TAA	70.4	-0.0811	-0.122	172(LNR6)
*atp6*	H	19034 - 19744	711	ATG	TAG	59.5	-0.0963	-0.126	2

Genes were labelled as outlined in the abbreviations section. AT skew = (A% - T%)/(A% + T%); GC skew = (G% - C%)/(C% + G%).
¹ truncated stop codon, which is possibly completed via post-transcriptional adenylation;
² unassigned nucleotides (positive values) or overlapped nucleotides (negative values) between two adjacent genes with large non-coding regions outlined;
³ initiation or termination positions of ribosomal RNAs defined by adjacent gene boundaries.

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ISSN: 1471-2164

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