Journal Name: Molecular Biology Reports

The complete mitochondrial genome of dhole Cuon alpinus: phylogenetic analysis and dating evolutionary divergence within Canidae

Journal name: Molecular Biology Reports

Authors:Lei Chen·Honghai Zhang()

Affiliation:College of Life Science, Qufu Normal University, Qufu 273165, China

Corresponding author: e-mail:

Table 1 Primers designed for amplifying and sequencing the complete mitochondrial genome of dhole (Cuon alpinus) in the LA-PCR

Primer No. / Product lenght(bp) / Uptream primer sequence(5′→3′) / Downstream primer sequence(5′→3′)
1-F/R / 3275 / TCCCTCTAGAGGAGCCTGTTC / GGGTATGGGCCCGATAGCTT
2-F/R / 3311 / GGCGGATAAAAGAGTTACTTTGATAGAG / GCGAATTTAACTTTGACAAAGTCATGT
3-F/R / 3337 / GAAGAAAGGAAGGAATCGAACC / GCGTAGGGATGATAATTTTTAGCATT
4-F/R / 3904 / GTATTTGCTGCCTGCGAAGC / TAGTGGTGGGATTGGTTGTGC
5-F/R / 3534 / GGGTATTGCTCAGTAGCCATAGC / GGTTTGCTGAAGATGGCGGTATAT

Table 2 Primers designed for amplifying and sequencing the complete mitochondrial genome of dhole (Cuon alpinus) in the Sub-PCR

Primer No. / Product lenght(bp) / Uptream primer sequence(5′→3′) / Downstream primer sequence(5′→3′)
1-F/R / 1654 / TCCCTCTAGAGGAGCCTGTTC / TCCGAGGTCACCCCAACC
2-F/R / 1740 / GACGAGAAGACCCTATGGAGC / GGGTATGGGCCCGATAGCTT
3-F/R / 1727 / GGCGGATAAAAGAGTTACTTTGATAGAG / GCCTACTATACCGGCTCATGC
4-F/R / 1593 / GCTCAGCCATTTTACCTATGTTC / GCGAATTTAACTTTGACAAAGTCATGT
5-F/R / 1869 / GAAGAAAGGAAGGAATCGAACC / GCGAAGAGTTGTAGTGAAATCATAT
7-F/R / 1591 / GCTACCTAATGACCCACCAAAC / GCGTAGGGATGATAATTTTTAGCATT
8-F/R / 1673 / GTATTTGCTGCCTGCGAAGC / CGCTTATCTGGAGTTGCACC
9-F/R / 2348 / CCGCAAGAACTGCTAATTCATG / TAGTGGTGGGATTGGTTGTGC
10-F/R / 1570 / GGGTATTGCTCAGTAGCCATAGC / GCAGAATTTCAGCTTTGGGTG
11-F/R / 2087 / CGCGATGAAGAGTCTTTGTAGTAT / GGTTTGCTGAAGATGGCGGTATAT

Table 3Species used as the family representatives for the phylogenic analysis in this study

Family / Genus / Scientific name / Common name / Genbank No.
Canidae
Canis
Canis latrans / coyote / NC_008093
Canis lupus lupus / Eurasian wolf / NC_009686
Canis lupus chanco / Mongolian wolf / GQ_374438
Canis lupus laniger / Tibetan wolf / NC_011218
Canis lupus familiaris / domestic dog / NC_002008
Cuon
Cuon alpinus / dhole / NC_013445
Vulpes
Vulpes vulpes / red fox / NC_008434
Nyctereutes
Nyctereutes procyonoides / raccoon dog / GU_256221
Ursidae
Ursus
Ursus arctos / brown bear / NC_003427

Table 4 The characteristics ofdhole(Cuon alpinus)mitochondrial genome protein-coding genes

Gene / Position / Size/bp / Interval(+)/Overlap(-) / Base composition (%) / Codons / Strand
From / To / A / C / G / T / Start / Stop
ND1 / 2751 / 3706 / 956 / 30.1 / 28.7 / 11.8 / 29.4 / ATG / TAA / H
ND2 / 3918 / 4958 / 1041 / -2 / 33.4 / 27.2 / 10.9 / 28.5 / ATA / TAG / H
COX I / 5348 / 6892 / 1545 / -3 / 26.9 / 23.4 / 18.0 / 31.7 / ATG / TAA / H
COX II / 7033 / 7716 / 684 / +16 / 32.3 / 23.8 / 13.9 / 30.0 / ATG / TAA / H
ATP8 / 7802 / 8005 / 204 / -43 / 34.3 / 28.9 / 9.3 / 27.5 / ATG / TAA / H
ATP6 / 7963 / 8643 / 681 / -1 / 27.9 / 26.1 / 13.1 / 32.9 / ATG / TAA / H
COX III / 8643 / 9426 / 784 / -2 / 26.8 / 26.0 / 15.3 / 31.9 / ATG / TA_ / H
ND3 / 9495 / 9840 / 346 / +1 / 32.4 / 24.3 / 11.8 / 31.5 / ATA / TA_ / H
ND4L / 9913 / 10209 / 297 / -7 / 31.3 / 19.9 / 12.5 / 36.4 / ATG / TAA / H
ND4 / 10203 / 11580 / 1378 / 30.7 / 26.4 / 11.5 / 31.4 / ATG / T__ / H
ND5 / 11780 / 13600 / 1821 / -17 / 30.6 / 26.1 / 12.1 / 31.2 / ATA / TAA / H
ND6 / 13584 / 14111 / 528 / 40.2 / 27.3 / 10.2 / 22.3 / ATG / TAA / L
CYT b / 14185 / 15324 / 1140 / 29.6 / 26.6 / 13.9 / 29.9 / ATG / AGA / H

Table 5 The characteristics of dhole (Cuon alpinus)mitochondrial genome tRNA and rRNA genes

Gene / Position / Size/bp / Strand / Gene / Position / Size/bp / Strand
From / To / From / To
tRNA-Phe / 1 / 69 / 69 / H / tRNA-Tyr / 5280 / 5346 / 67 / L
12S rRNA / 70 / 1024 / 955 / H / tRNA-Ser(UCN) / 6890 / 6958 / 69 / L
tRNA-Val / 1025 / 1091 / 67 / H / tRNA-Asp / 6965 / 7032 / 68 / H
16S rRNA / 1092 / 2672 / 1581 / H / tRNA-Lys / 7734 / 7800 / 67 / H
tRNA-Leu(UUR) / 2673 / 2747 / 75 / H / tRNA-Gly / 9427 / 9494 / 68 / H
tRNA-Ile / 3707 / 3775 / 69 / H / tRNA-Arg / 9842 / 9912 / 71 / H
tRNA-Gln / 3773 / 3846 / 74 / L / tRNA-His / 11581 / 11649 / 69 / H
tRNA-Met / 3848 / 3917 / 70 / H / tRNA-Ser(AGY) / 11650 / 11709 / 60 / H
tRNA-Trp / 4957 / 5024 / 68 / H / tRNA-Leu(TAG) / 11710 / 11779 / 70 / H
tRNA-Ala / 5038 / 5106 / 69 / L / tRNA-Glu / 14112 / 14180 / 69 / L
tRNA-Asn / 5108 / 5179 / 72 / L / tRNA-Thr / 15325 / 15394 / 70 / H
tRNA-Cys / 5214 / 5279 / 66 / L / tRNA-Pro / 15394 / 15459 / 66 / L

Fig. 1 LA-PCR (A) and Sub-PCR (B) product covering the complete mitochondrial genome of dhole (Cuon alpinus)

Fig. 2 (A) Secondary structure of tRNA –Phe. 21 ofdhole (Cuon alpinus)mitochondrial genome tRNA genes could be folded into a cloverleaf secondary structure like tRNA –Phe. (B) Secondary structure of tRNA-Ser (AGY). It was an exception which missed the dihydrouridine arm.