Sequence analysis of four caprine mitochondria DNA lineages

Figures & data

Table 1 Information of the samples.

Lineage	Breed	Sample size	Resource
A	Langkazi	1	Tibet
B	Yunling Black	1	Yunnan
C	Wuzhumuqin White Cashmere	1	Neimeng
D	Tsaidam Cashmere	1	Qinghai

Table 2 Amino acid substitutions among goat lineages.

Gene	Position	SNP of 4 lineage				Amino acid substitutions	Results of polyphen	PSIC score
A	B	C	D
ND1	2943	T	T	C	T	Ile - Thr	Benign	0.089
COX1	6573	A	A	A	G	Ile - Val	Benign	0.233
COX2	7051	A	G	G	A	Thr - Ala	Benign	0.055
COX2	7462	A	A	A	G	Ile - Val	Benign	0.356
ATP6	8054	G	A	A	A	Val - Ile	Benign	0.361
ATP6	8103	G	G	A	G	Ser - Asn	Benign	0.180
COX3	8729	C	T	C	C	Ala - Val	Benign	0.400
COX3	9060	T	T	C	T	Met - Thr	Benign	0.807
ND3	9546	T	T	C	T	Val - Ala	Benign	0.276
ND4L	10000	A	A	A	G	Ile - Val	Benign	0.619
ND5	11807	T	T	T	C	Met - Thr	Benign	0.991
ND5	11870	G	A	G	G	Cys - Tyr	Benign	0.112
ND5	12004	G	G	G	A	Val - Met	Benign	0.851
ND5	12190	A	A	G	A	Ile - Val	Benign	1.282
ND5	12838	G	G	G	A	Ala - Thr	Benign	0.443
ND5	13476	A	C	A	A	Met - Ile	Benign	0.083
ND6	13581	T	G	G	G	Val - Gly	Benign	0.334
CYTB	14161	T	T	C	T	Ile - Thr	Benign	0.694

Table 3 Single nucleotide polymorphisms in goat mitochondrial RNA.

Gene	Position lineage	Variation substitution	Base	Domain
tRNA	Ile	3738	D	A-G	Connection of anticodon arm and T arm
	Ala	5083
L strand	D	A-G	Stems (principle of G-U pairing)
Trp	4962	B	A-G	D loop
Gly	9415	D	A-G	Connection of anticodon arm and D arm
His	11567	C	A-G	Connection of anticodon arm and D arm
Leu	11689	B	G-A	D loop
Leu	11700	B	A-G	Connection of anticodon arm and D arm
12SrRNA	165	C	T-C	Loops
203	B	C-T	Loops
211	C	C-T	Loops
292	D	G-A	Loops
16SrRNA	1190	C	T-C	Loops
1367	C	C-T	Loops
1848	BC	T-C	Loops
2090	BC	T-C	Loops
2117	D	T-C	Unstructured single strand
2206	D	T-C	Loops
2415	B	G-A	Loops
2515	B	C-T	Loops
2637	D	A-G	Stems (principle of G-U pairing)

Figure 1 Radio-protective mechanism of melatonin.

Table 4 Estimates of time of divergence between mtDNA clades present in different populations.

RNA	Mammalian mtDNA specific mutation rate°	Estimated time of divergence^#
		Goat vs sheep	Goat/sheep vs cow/yak	Goat/sheep vs pig	Goat/sheep vs horse/donkey
12rRNA	3.4±1.2	9.53	17.63	27.69	33.57
16rRNA	4.9±1.4	9.86	13.25	20.55	21.52
tRNA	3.4±1.1	8.68	12.83	26.85	29.08

° Estimated rate of nucleotide substitution (substitutions/site/year×10⁻⁹) specific for each functional component of the mammalian mtDNA genome (Pesole et al., 1999).

# The time since divergence (years×10⁶) was estimated on the basis of data from each functional component using the pairwise sequence divergence values appearing in Tables 3–11 in Wu, 2008.

Appendix Table 1 Primer sequence, corresponding polymerase chain reaction product size and position.

Code	Primer sequence	Product size	Position	Temperature
G1	5‘ CGCCCTCCAAATCAATAA 3’	639	144–782	53
5‘ CCCATTTCTTCCCATTCC 3’
G2	5‘ CCCATTTCTTCCCATTCC 3’	621	765–1391	52
5‘ TTGCCACATAGATGAGTTG 3’
G3	5‘ CAACTCATCTATGTGGCA 3’	991	1373–2363	53.2
5‘ TAGGGTAACTTGTTCCGT 3’
G4	5‘ AGTTTTGGTTGGGGTGAC 3’	1405	2237–3641	56
5‘ ATAGGGCCAGTGTTAGGG 3’
G5	5‘ TACCCCCGATTCCGTTAC 3’	1421	3569–4989	56
5‘ TTAGGGCTTTGAAGGCTC 3’
G6	5‘ ACTCACACCAATCCTCTCAAT 3’	1359	4919–6277	56
5‘ CCAGTTGGGATAGCGATAAT 3’
G7	5‘ GATACACGGGCTTACTTCAC 3’	1227	6225–7451	56.8
5‘ ATGGGTAGTACAACTCGGTT 3’
G8	5‘ AAACCTGGAGAACTACGA 3’	1427	7399–8825	55
5‘ GGAGTATGGTGACCTTGG 3’
G9	5‘ ATACCAATGATGACGAGATGTG3’	1155	8769–9923	56
5‘ AGAGATACTGCGAATGCTGTTA 3’
G10	5‘ AACAGCATTCGCAGTATCT 3’	1182	9903–11084	55
5‘ GGGTGTCTGGATAAGGATG 3’
G11	5‘ CCTGAAATCACTCATCGC 3’	1247	11009–12255	55
5‘ TTGTAGGGCTGCTGTGTT 3’
G12	5‘ GGTGGTATGGACGAGCAGA 3’	1148	12215–13362	58
5‘ GTAGGGCATTAAGCGGTGT 3’
G13	5‘ TTGGAAGCCTTTTCACAG 3’	1289	13121–14409	54
5‘ CTCCGTTTGCGTGTATGT 3’
CB	5‘ AATGATATGAAAAACCATC 3’	1344	14106–15449	50
5‘ CCACTATTAACCACATCTA 3’
DL	5‘ AGACTCAAGGAAGAAGCCA 3’	1438	15359–16640	55
5‘ GATTTGGAGGGCGTTACT 3’	1–156

PesoleG. GissiC. De ChiricoA. SacconeC. 1999 Nucleotide substitution rate of mammalian mitochondrial genomes J. Mol. Evol 48 427 434

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WuY.P. 2008 Diversity and phylogenetic relationships of some Chinese goat breeds Chinese Academy of Agricultural Sciences Publ. Beijing, China

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