http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971250
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome sequence of Neovison vison (Carnivora: Mustelidae) Wei-li Sun1,2, Shao-jing Wang3, Zhuo Wang1,2, Han-lu Liu1,2, Wei Zhong1,2, Ya-han Yang1,2, and Guang-yu Li1,2 Institute of Special Animal and Plant Science, Chinese Academy of Agricultural Sciences (CAAS), Changchun, P.R. China, 2State Key Lab for Molecular Biology of Special Economic Animals, Changchun, P.R. China, and 3Tianjin Maianzhen Biotech Ltd, Tianjin, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 10/22/14 For personal use only.
1
Abstract
Keywords
The phylogenetic and taxonomic position of the American mink Neovison vison have long been unclear. In this paper, the complete mitogenome of N. vison was sequenced and characterized. The total length was 16,594 bp and typically consists of 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNA, a large control region (CR) and a light-strand replication origin (OL). Gene contents, locations, and arrangements were identical to those of typical vertebrate. The overall base composition is 33.6%, 25.4%, 27.8% and 13.3% for A, C, T and G, respectively, with a moderate bias on AT content (61.4%). This result is expected to provide useful molecular data and contribute to further taxonomic and phylogenetic studies of Mustelidae and Carnivora.
American mink, Mustelinae, mitogenome, phylogeny
The American mink (Neovison vison, formerly Mustela vison) is a member of the Mustelidae in the order Carnivora. It is a small commercial mammalian for its valuable fur. This species and its congeners are a kind of semi-aquatic carnivorous mustelid, which prey on crayfish, crabs, and fish (Yoshimura et al., 2014). At present, researchers mainly work on the feeding habits, living environment, diet and nutrient digestibility (Gugolek et al., 2013; Magnusdottir et al., 2014; Zschille et al., 2014). However, the phylogenetic and taxonomic position of N. vison have long been unclear (Abramov, 1999). In this study, we determined the complete mitogenome of N. vison, expecting to provide molecular data and contribute to the further systematic evolution analysis of the family Mustelidae and Carnivora. The specimen was collected from Jilin, China. Fifteen pairs of primers were designed according to previously reported mammal mitogenomes (Huang et al., 2014; Koepfli & Wayne, 1998). The total length was 16,594 bp (GenBank accession No. KM488625), including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes (12S and 16S), as well as a putative control region (CR) and a light-strand replication origin (OL). Most of these genes were encoded on the H-strand, except the ND6 and seven tRNA genes (Table 1). A total of 19 base pairs in nine intergenic spacers were found ranging from 1 to 5 bp. Twelve overlapping sites (a total of 61 bp) were observed, including the four notable overlappings between
History Received 9 September 2014 Revised 19 September 2014 Accepted 26 September 2014 Published online 16 October 2014
ATP8 and ATP6 (by 4 bp), ATP6 and COX3 (by 1 bp), ND4L and ND4 (by 7 bp), and ND5 and ND6 (by 17 bp). The 13 proteincoding genes encode 3790 amino acids in total. The most frequently used amino acid was Leucine (15.47%) while Cysteine acid (0.63%) was the least frequently used one. Nine proteincoding genes used the initiation codon ATG while ATP6, ND3 and ND5 use ATA, and ND2 uses an unusual ATC. Most of them had TAA or TAG as the stop codon, except cytb used AGA and COX3 used an incomplete stop codon TA and ND4 used T. The 12S rDNA and 16S rDNA were 960 bp and 1569 bp, respectively, and both were located in the typical positions between tRNA-Phe and tRNALeu(UUA), separated by tRNA-Val. The 22 tRNA genes were interspersed between rRNAs and protein-coding genes, with sizes ranging from 62 bp (tRNA-Ser(UGC)) to 75 bp (tRNA-Leu(UUA)). The 48 bp OL was located between tRNA-Asn and tRNA-Cys genes in the WANCY region and has the potential to fold into a stable stem-loop structure with a 13 bp stem and a 14 nucleotide loop. The highly conserved block of 50 -GCCGG-30 is substituted with 50 -CCCGG-30 . The CR typically situates between tRNA-Pro and tRNA-Phe genes with 1130 bp in length. The overall base composition was calculated by MEGA 5 (Tamura et al., 2011): 33.6%, 25.4%, 27.8% and 13.3% for A, C, T and G, respectively, with a moderate bias on AT content (61.4%), similar to other vertebrate mitochondrial genomes (Ryu & Hwang, 2011; Zhang et al., 2014; Zhu et al., 2013).
Correspondence: Guang-yu Li, Institute of Special Animal and Plant Science, Chinese Academy of Agricultural Sciences (CAAS), Changchun 130112, P.R. China. Tel/Fax: +86 43181919515. E-mail: [email protected]
2
W. -L. Sun et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Features of the mitochondrial genome of N. vison.
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 10/22/14 For personal use only.
Position Gene
From
To
Length (bp)
tRNA-Phe 12S RNA tRNA-Val 16S RNA tRNA-LeuUUA ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn OL tRNA-Cys tRNA-Tyr COX1 tRNA-SerUCA tRNA-Asp COX2 tRNA-Lys ATP8 ATP6 COX3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-SerUGC tRNA-LeuGUA ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro D-loop
1 70 1030 1098 2667 2744 3700 3766 3841 3910 4952 5028 5098 5165 5204 5271 5340 6886 6960 7027 7714 7782 7982 8623 9407 9476 9823 9891 10,181 11,559 11,628 11,690 11,760 13,582 14,116 14,189 15,329 15,396 15,462
69 1029 1097 2666 2741 3700 3768 3839 3909 4953 5019 5096 5170 5212 5270 5338 6884 6954 7026 7710 7780 7985 8623 9407 9475 9832 9890 10,187 11,558 11,627 11,689 11,759 13,598 14,115 14,184 15,328 15,396 15,461 16,591
69 960 68 1569 75 957 69 74 69 1044 68 69 73 48 67 68 1545 69 67 684 67 204 642 785 69 357 68 297 1378 69 62 70 1839 534 69 1140 68 66 1130
Amino acid
Start/Stop codon
Anticodon GAA TAC TAA
318
ATG/TAA GAT TTG CAT
347
ATC/TAG TCA TGC GTT GTA GTA
514
ATG/TAA TGA GTC
227
ATG/TAA
67 213 261
ATG/TAA ATA/TAA ATG/TA
118
ATA/TAG
98 459
ATG/TAA ATG/T
TTT
TCC TCG GTG GCT TAG 612 177
ATA/TAA ATG/TAA
379
ATG/AGA
TTC TGT TGG
Intergenic region* 0 0 0 0 2 1 3 1 0 2 8 1 6 9 0 1 1 5 0 3 1 4 1 1 0 10 0 7 0 0 0 0 17 0 4 0 1 0 0
Strand H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H H L L H H L H
*Intergenic region: non-coding bases between the feature on the same line and the line below, with a negative number indicating an overlap.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Abramov AV. (1999). A taxonomic review of the genus Mustela (Mammalia, Carnivora). Zoosystematica Rossica 8:357–64. Gugolek A, Zalewski D, Strychalski J, Konstantynowicz M. (2013). Food transit time, nutrient digestibility and nitrogen retention in farmed and feral American mink (Neovison vison) – A comparative analysis. J Anim Physiol An N 97:1030–5. Huang J, Yang B, Yan CC, Yang CZ, Tu FY, Zhang XY, Yue BS. (2014). Phylogenetic analysis of the Mustela altaica (Carnivora: Mustelidae) based on complete mitochondrial genome. Mitochondrial DNA 25: 255–6. Koepfli KP, Wayne RK. (1998). Phylogenetic relationships of otters (Carnivora: Mustelidae) based on mitochondrial cytochrome b sequences. J Zool 246:401–16. Magnusdottir R, von Schmalensee M, Stefansson RA, Macdonald DW, Hersteinsson P. (2014). A foe in woe: American mink (Neovison
vison) diet changes during a population decrease. Mamm Biol 79: 58–63. Ryu SH, Hwang UW. (2011). Complete mitochondrial genome of the Baikal teal Anas formosa (Aves, Anseriformes, Anatidae). Mitochondrial DNA 22:74–6. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9. Yoshimura K, Fukue Y, Kishimoto R, Shindo J, Kageyama I. (2014). Comparative morphology of the lingual papillae and their connective tissue cores in the tongue of the American mink, Neovison vison. Zool Sci 31:292–9. Zhang HH, Zhang J, Chen L, Liu GS. (2014). The complete mitochondrial genome of Chinese Shinjang wolf. Mitochondrial DNA 25: 106–8. Zhu SR, Ma KY, Xing ZJ, Xie N, Wang YX, Wang Q, Li JL. (2013). The complete mitochondrial genome of Channa argus, Channa maculata and hybrid snakehead fish [Channa maculata (,) Channa argus (
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome sequence of Neovison vison (Carnivora: Mustelidae) Wei-li Sun1,2, Shao-jing Wang3, Zhuo Wang1,2, Han-lu Liu1,2, Wei Zhong1,2, Ya-han Yang1,2, and Guang-yu Li1,2 Institute of Special Animal and Plant Science, Chinese Academy of Agricultural Sciences (CAAS), Changchun, P.R. China, 2State Key Lab for Molecular Biology of Special Economic Animals, Changchun, P.R. China, and 3Tianjin Maianzhen Biotech Ltd, Tianjin, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 10/22/14 For personal use only.
1
Abstract
Keywords
The phylogenetic and taxonomic position of the American mink Neovison vison have long been unclear. In this paper, the complete mitogenome of N. vison was sequenced and characterized. The total length was 16,594 bp and typically consists of 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNA, a large control region (CR) and a light-strand replication origin (OL). Gene contents, locations, and arrangements were identical to those of typical vertebrate. The overall base composition is 33.6%, 25.4%, 27.8% and 13.3% for A, C, T and G, respectively, with a moderate bias on AT content (61.4%). This result is expected to provide useful molecular data and contribute to further taxonomic and phylogenetic studies of Mustelidae and Carnivora.
American mink, Mustelinae, mitogenome, phylogeny
The American mink (Neovison vison, formerly Mustela vison) is a member of the Mustelidae in the order Carnivora. It is a small commercial mammalian for its valuable fur. This species and its congeners are a kind of semi-aquatic carnivorous mustelid, which prey on crayfish, crabs, and fish (Yoshimura et al., 2014). At present, researchers mainly work on the feeding habits, living environment, diet and nutrient digestibility (Gugolek et al., 2013; Magnusdottir et al., 2014; Zschille et al., 2014). However, the phylogenetic and taxonomic position of N. vison have long been unclear (Abramov, 1999). In this study, we determined the complete mitogenome of N. vison, expecting to provide molecular data and contribute to the further systematic evolution analysis of the family Mustelidae and Carnivora. The specimen was collected from Jilin, China. Fifteen pairs of primers were designed according to previously reported mammal mitogenomes (Huang et al., 2014; Koepfli & Wayne, 1998). The total length was 16,594 bp (GenBank accession No. KM488625), including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes (12S and 16S), as well as a putative control region (CR) and a light-strand replication origin (OL). Most of these genes were encoded on the H-strand, except the ND6 and seven tRNA genes (Table 1). A total of 19 base pairs in nine intergenic spacers were found ranging from 1 to 5 bp. Twelve overlapping sites (a total of 61 bp) were observed, including the four notable overlappings between
History Received 9 September 2014 Revised 19 September 2014 Accepted 26 September 2014 Published online 16 October 2014
ATP8 and ATP6 (by 4 bp), ATP6 and COX3 (by 1 bp), ND4L and ND4 (by 7 bp), and ND5 and ND6 (by 17 bp). The 13 proteincoding genes encode 3790 amino acids in total. The most frequently used amino acid was Leucine (15.47%) while Cysteine acid (0.63%) was the least frequently used one. Nine proteincoding genes used the initiation codon ATG while ATP6, ND3 and ND5 use ATA, and ND2 uses an unusual ATC. Most of them had TAA or TAG as the stop codon, except cytb used AGA and COX3 used an incomplete stop codon TA and ND4 used T. The 12S rDNA and 16S rDNA were 960 bp and 1569 bp, respectively, and both were located in the typical positions between tRNA-Phe and tRNALeu(UUA), separated by tRNA-Val. The 22 tRNA genes were interspersed between rRNAs and protein-coding genes, with sizes ranging from 62 bp (tRNA-Ser(UGC)) to 75 bp (tRNA-Leu(UUA)). The 48 bp OL was located between tRNA-Asn and tRNA-Cys genes in the WANCY region and has the potential to fold into a stable stem-loop structure with a 13 bp stem and a 14 nucleotide loop. The highly conserved block of 50 -GCCGG-30 is substituted with 50 -CCCGG-30 . The CR typically situates between tRNA-Pro and tRNA-Phe genes with 1130 bp in length. The overall base composition was calculated by MEGA 5 (Tamura et al., 2011): 33.6%, 25.4%, 27.8% and 13.3% for A, C, T and G, respectively, with a moderate bias on AT content (61.4%), similar to other vertebrate mitochondrial genomes (Ryu & Hwang, 2011; Zhang et al., 2014; Zhu et al., 2013).
Correspondence: Guang-yu Li, Institute of Special Animal and Plant Science, Chinese Academy of Agricultural Sciences (CAAS), Changchun 130112, P.R. China. Tel/Fax: +86 43181919515. E-mail: [email protected]
2
W. -L. Sun et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Features of the mitochondrial genome of N. vison.
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 10/22/14 For personal use only.
Position Gene
From
To
Length (bp)
tRNA-Phe 12S RNA tRNA-Val 16S RNA tRNA-LeuUUA ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn OL tRNA-Cys tRNA-Tyr COX1 tRNA-SerUCA tRNA-Asp COX2 tRNA-Lys ATP8 ATP6 COX3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-SerUGC tRNA-LeuGUA ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro D-loop
1 70 1030 1098 2667 2744 3700 3766 3841 3910 4952 5028 5098 5165 5204 5271 5340 6886 6960 7027 7714 7782 7982 8623 9407 9476 9823 9891 10,181 11,559 11,628 11,690 11,760 13,582 14,116 14,189 15,329 15,396 15,462
69 1029 1097 2666 2741 3700 3768 3839 3909 4953 5019 5096 5170 5212 5270 5338 6884 6954 7026 7710 7780 7985 8623 9407 9475 9832 9890 10,187 11,558 11,627 11,689 11,759 13,598 14,115 14,184 15,328 15,396 15,461 16,591
69 960 68 1569 75 957 69 74 69 1044 68 69 73 48 67 68 1545 69 67 684 67 204 642 785 69 357 68 297 1378 69 62 70 1839 534 69 1140 68 66 1130
Amino acid
Start/Stop codon
Anticodon GAA TAC TAA
318
ATG/TAA GAT TTG CAT
347
ATC/TAG TCA TGC GTT GTA GTA
514
ATG/TAA TGA GTC
227
ATG/TAA
67 213 261
ATG/TAA ATA/TAA ATG/TA
118
ATA/TAG
98 459
ATG/TAA ATG/T
TTT
TCC TCG GTG GCT TAG 612 177
ATA/TAA ATG/TAA
379
ATG/AGA
TTC TGT TGG
Intergenic region* 0 0 0 0 2 1 3 1 0 2 8 1 6 9 0 1 1 5 0 3 1 4 1 1 0 10 0 7 0 0 0 0 17 0 4 0 1 0 0
Strand H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H H L L H H L H
*Intergenic region: non-coding bases between the feature on the same line and the line below, with a negative number indicating an overlap.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Abramov AV. (1999). A taxonomic review of the genus Mustela (Mammalia, Carnivora). Zoosystematica Rossica 8:357–64. Gugolek A, Zalewski D, Strychalski J, Konstantynowicz M. (2013). Food transit time, nutrient digestibility and nitrogen retention in farmed and feral American mink (Neovison vison) – A comparative analysis. J Anim Physiol An N 97:1030–5. Huang J, Yang B, Yan CC, Yang CZ, Tu FY, Zhang XY, Yue BS. (2014). Phylogenetic analysis of the Mustela altaica (Carnivora: Mustelidae) based on complete mitochondrial genome. Mitochondrial DNA 25: 255–6. Koepfli KP, Wayne RK. (1998). Phylogenetic relationships of otters (Carnivora: Mustelidae) based on mitochondrial cytochrome b sequences. J Zool 246:401–16. Magnusdottir R, von Schmalensee M, Stefansson RA, Macdonald DW, Hersteinsson P. (2014). A foe in woe: American mink (Neovison
vison) diet changes during a population decrease. Mamm Biol 79: 58–63. Ryu SH, Hwang UW. (2011). Complete mitochondrial genome of the Baikal teal Anas formosa (Aves, Anseriformes, Anatidae). Mitochondrial DNA 22:74–6. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9. Yoshimura K, Fukue Y, Kishimoto R, Shindo J, Kageyama I. (2014). Comparative morphology of the lingual papillae and their connective tissue cores in the tongue of the American mink, Neovison vison. Zool Sci 31:292–9. Zhang HH, Zhang J, Chen L, Liu GS. (2014). The complete mitochondrial genome of Chinese Shinjang wolf. Mitochondrial DNA 25: 106–8. Zhu SR, Ma KY, Xing ZJ, Xie N, Wang YX, Wang Q, Li JL. (2013). The complete mitochondrial genome of Channa argus, Channa maculata and hybrid snakehead fish [Channa maculata (,) Channa argus (
