http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1043539
MITOGENOME ANNOUNCEMENT
Sequencing and analysis of the complete mitochondrial genome of Amur minnow from China Shuai Zhao, Xiaomin Han, and Chunzhu Xu
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/06/15 For personal use only.
College of Life Science, Northeast Agricultural University, Harbin, PR China
Abstract
Keywords
The complete mitogenome sequence of Amur minnow (Rhynchocypris lagowskii) was determined using long PCR. The genome was 16,594 bp in length and contained 13 proteincoding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The overall base composition of the heavy strand is A (28.60%), C (26.32%), T (27.40%), and G (17.68%). The control region was 927 bp in length and the A + T content of the region was 63.32%. The extended termination-associated sequence domain, the central conserved domain, and the conserved sequence block domain are defined in the mitochondrial genome control region of Amur minnow. Mitochondrial genomes analyses based on maximum parsimony (MP), neighbor-joining (NJ), and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 15 Cyprinidae species. It appeared that no less than two major phyletic lineages were present in Leuciscinae. The main clades within the Leuciscinae supported are: A clade is the Tribolodon. A clade (Rhynchocypris) with the Oreoleuciscus as the sister taxon to Tribolodon was supported by bootstrap values of 49%. The five different geographical populations of the R. lagowskii formed a paraphyletic group with the high bootstrap value (45%) in all examinations.
Amur minnow, control region, mitogenome, phylogenetic tree
The genus Rhynchocypris (Teleostei, Cypriniformes, Cyprinidae) is a group of small cold water freshwater fishes, mainly distributed in East Asia including the Far East region of Russia, China, Mongolia, Korea, and Japan (Xu et al., 2014). In this paper, the complete mitochondrial genome of Amur minnow was sequenced using a primer walking strategy and the long and accurate PCR, with five pairs of long PCR primers and with 15 pairs of sub-PCR primers. A muscle sample was obtained from the Amur minnow (Rhynchocypris lagowskii) captured from the Lesser Khingan Mountains in Heilongjiang Province, China (47 030 3900 N, 128 590 3300 E). The mitochondrial genome has a circular double-stranded DNA sequence that is 16,594 bp long including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. The accurate annotated mitochondrial genome sequence was submitted to GenBank with accession number KR091310. The arrangement of the multiple genes is in line with other Cyprinidae species (Chen et al., 2013; Hwang et al., 2014; Kim et al., 2006) and most Osteichthyes (Campbell et al., 2014; Yu et al., 2014a,b). The control region of Amur minnow mitochondrial genome was 927 bp in length and the A + T content of the region was
Correspondence: Dr. Chunzhu Xu, College of Life Science, Northeast Agricultural University, No. 59 Mucai Street Xiangfang District, Harbin 150030, Heilongjiang, China. Tel: +86 451 55190741. Fax: +86 451 55190413. E-mail: [email protected]
History Received 14 April 2015 Accepted 18 April 2015 Published online 1 June 2015
63.32%. Three domains were defined in Amur minnow mitochondrial genome control region: the extended terminationassociated sequence (ETAS) domain, the central conserved domain (CD), and the conserved sequence block (CSB) domain. Three CSBs were found in the CSB domain and they were located in positions 16,088–16,103, 16,357–16,373, and 16,400–16,417. They were similar to CSBs of other fishes and mammals species sequences (Wei et al., 2014; Zhang et al., 2009). The total length of the protein-coding gene sequences was 11,418 bp. Most protein-coding genes initiate with ATG except for COX1, which began with GTG. Seven protein-coding genes ended with complete termination codons TAA (ND1, COX1, ATP6, ND4L, ND5, and ND6) and TAG (ATP8). The incomplete stop codons (T–) were used in ND2, COX2, COX3, ND3, ND4, and Cyt b. The length of tRNA genes varied from 68 to 76 bp. Most Amur minnow mitochondrial genes were encoded on the H strand, except for the ND6 gene and eight tRNA genes, which were encoded on the L strand. The total base composition of Amur minnow mitochondrial genome was A (28.60%), C (26.32%), T (27.40%), and G (17.68%). Mitochondrial genomes analyses based on maximum parsimony (MP), neighbor-joining (NJ), and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 15 Cyprinidae species. The phylogram obtained from NJ method is shown in Figure 1. It appeared that no less than two major phyletic lineages were present in Leuciscinae. The main clades within the Leuciscinae supported are: A clade is the Tribolodon. A clade (Rhynchocypris) with the Oreoleuciscus as
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/06/15 For personal use only.
2
S. Zhao et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic tree generated using the neighbor-joining method based on the complete mitochondrial genomes. Genbank accession numbers for each taxa are the following: Rhynchocypris lagowskii HL (KR091310; in this study), Rhynchocypris lagowskii JY (AP009148), Rhynchocypris lagowskii UL (AP009147), Rhynchocypris lagowskii TM1 (KC967217), Rhynchocypris lagowskii TM2 (KF734881), Rhynchocypris perenurus (AP009061), Rhynchocypris perenurus (AP009150), Oreoleuciscus potanini (AB626851), Tribolodon hakonensis (AB626855), Tribolodon sachalinensis (AB626856), Tribolodon nakamurai (AB218896), Tribolodon brandtii (AB626853), Rhynchocypris kumgangensis (JQ675733), Rhodeus sericeus (KM052222; in this study), and Rhodeus lighti (NC_024885).
the sister taxon to Tribolodon was supported by bootstrap values of 49%. The five different geographical populations of the R. lagowskii formed a paraphyletic group with the high bootstrap value (45%) in all examinations.
Declaration of interest This research was supported by the Special Fund for Talent Cultivation From National Scientific Base for Basic Scientific Research and Teaching Talent Cultivation of Northeast Agricultural University in China (J1210069) and the Natural Science Foundation of Heilongjiang Province (QC2013C016).
References Campbell MA, Lo´pez JA, Satoh TP, Chen WJ, Miya M. (2014). Mitochondrial genomic investigation of flatfish monophyly. Gene 551: 176–82. Chen Y, Cheng QQ, Qiao HY, Zhu YX, Chen WM, Ren GJ. (2013). The complete mitochondrial genome sequence of Schizothorax wangchiachii (Cypriniformes: Cyprinidae). Mitochondrial DNA 24:353–5.
Hwang DS, Lee WO, Lee JS. (2014). Complete mitochondrial genome of the freshwater fish, Rhodeus suigensis (Cypriniformes, Cyprinidae). Mitochondrial DNA 25:5–6. Kim BC, Kang TW, Kim MS, Kim CB. (2006). The complete mitogenome of Rhodeus uyekii (Cypriniformes, Cyprinidae). DNA Sequence 17:181–6. Wei T, Zhang B, Sun YN. (2014). Structure comparison of control region in Stromateoidei and complete mitochondrial genome of the bluefin driftfish Psenes pellucidus (Perciformes, Nomeidae). Mitochondrial DNA 25:355–6. Xu W, Chen AH, Xia R, Fu CZ. (2014). Complete mitochondrial genome of Rhynchocypris cf. Lagowskii (Cypriniformes: Cyprinidae). Mitochondrial DNA 25:379–80. Yu JN, Kim S, Kwak M. (2014a). Complete mitochondrial genome sequence of a Korean Pungtungia herzi (Cypriniformes, Gobioninae). Mitochondrial DNA 25:414–15. Yu YY, Li YH, Wang WM, Zhou XY. (2014b). Complete mitochondrial genome of the natural triploid loach, Misgurnus anguillicaudatus (Teleostei: Cypriniformes: Cobitididae). Mitochondrial DNA 25: 353–4. Zhang HH, Xu CZ, Ma JZ. (2009). Structure of the mt DNA control region and phylogeny of the Mustelidae species. Acta Ecol Sin 29: 3585–92.
MITOGENOME ANNOUNCEMENT
Sequencing and analysis of the complete mitochondrial genome of Amur minnow from China Shuai Zhao, Xiaomin Han, and Chunzhu Xu
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/06/15 For personal use only.
College of Life Science, Northeast Agricultural University, Harbin, PR China
Abstract
Keywords
The complete mitogenome sequence of Amur minnow (Rhynchocypris lagowskii) was determined using long PCR. The genome was 16,594 bp in length and contained 13 proteincoding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The overall base composition of the heavy strand is A (28.60%), C (26.32%), T (27.40%), and G (17.68%). The control region was 927 bp in length and the A + T content of the region was 63.32%. The extended termination-associated sequence domain, the central conserved domain, and the conserved sequence block domain are defined in the mitochondrial genome control region of Amur minnow. Mitochondrial genomes analyses based on maximum parsimony (MP), neighbor-joining (NJ), and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 15 Cyprinidae species. It appeared that no less than two major phyletic lineages were present in Leuciscinae. The main clades within the Leuciscinae supported are: A clade is the Tribolodon. A clade (Rhynchocypris) with the Oreoleuciscus as the sister taxon to Tribolodon was supported by bootstrap values of 49%. The five different geographical populations of the R. lagowskii formed a paraphyletic group with the high bootstrap value (45%) in all examinations.
Amur minnow, control region, mitogenome, phylogenetic tree
The genus Rhynchocypris (Teleostei, Cypriniformes, Cyprinidae) is a group of small cold water freshwater fishes, mainly distributed in East Asia including the Far East region of Russia, China, Mongolia, Korea, and Japan (Xu et al., 2014). In this paper, the complete mitochondrial genome of Amur minnow was sequenced using a primer walking strategy and the long and accurate PCR, with five pairs of long PCR primers and with 15 pairs of sub-PCR primers. A muscle sample was obtained from the Amur minnow (Rhynchocypris lagowskii) captured from the Lesser Khingan Mountains in Heilongjiang Province, China (47 030 3900 N, 128 590 3300 E). The mitochondrial genome has a circular double-stranded DNA sequence that is 16,594 bp long including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. The accurate annotated mitochondrial genome sequence was submitted to GenBank with accession number KR091310. The arrangement of the multiple genes is in line with other Cyprinidae species (Chen et al., 2013; Hwang et al., 2014; Kim et al., 2006) and most Osteichthyes (Campbell et al., 2014; Yu et al., 2014a,b). The control region of Amur minnow mitochondrial genome was 927 bp in length and the A + T content of the region was
Correspondence: Dr. Chunzhu Xu, College of Life Science, Northeast Agricultural University, No. 59 Mucai Street Xiangfang District, Harbin 150030, Heilongjiang, China. Tel: +86 451 55190741. Fax: +86 451 55190413. E-mail: [email protected]
History Received 14 April 2015 Accepted 18 April 2015 Published online 1 June 2015
63.32%. Three domains were defined in Amur minnow mitochondrial genome control region: the extended terminationassociated sequence (ETAS) domain, the central conserved domain (CD), and the conserved sequence block (CSB) domain. Three CSBs were found in the CSB domain and they were located in positions 16,088–16,103, 16,357–16,373, and 16,400–16,417. They were similar to CSBs of other fishes and mammals species sequences (Wei et al., 2014; Zhang et al., 2009). The total length of the protein-coding gene sequences was 11,418 bp. Most protein-coding genes initiate with ATG except for COX1, which began with GTG. Seven protein-coding genes ended with complete termination codons TAA (ND1, COX1, ATP6, ND4L, ND5, and ND6) and TAG (ATP8). The incomplete stop codons (T–) were used in ND2, COX2, COX3, ND3, ND4, and Cyt b. The length of tRNA genes varied from 68 to 76 bp. Most Amur minnow mitochondrial genes were encoded on the H strand, except for the ND6 gene and eight tRNA genes, which were encoded on the L strand. The total base composition of Amur minnow mitochondrial genome was A (28.60%), C (26.32%), T (27.40%), and G (17.68%). Mitochondrial genomes analyses based on maximum parsimony (MP), neighbor-joining (NJ), and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 15 Cyprinidae species. The phylogram obtained from NJ method is shown in Figure 1. It appeared that no less than two major phyletic lineages were present in Leuciscinae. The main clades within the Leuciscinae supported are: A clade is the Tribolodon. A clade (Rhynchocypris) with the Oreoleuciscus as
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/06/15 For personal use only.
2
S. Zhao et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic tree generated using the neighbor-joining method based on the complete mitochondrial genomes. Genbank accession numbers for each taxa are the following: Rhynchocypris lagowskii HL (KR091310; in this study), Rhynchocypris lagowskii JY (AP009148), Rhynchocypris lagowskii UL (AP009147), Rhynchocypris lagowskii TM1 (KC967217), Rhynchocypris lagowskii TM2 (KF734881), Rhynchocypris perenurus (AP009061), Rhynchocypris perenurus (AP009150), Oreoleuciscus potanini (AB626851), Tribolodon hakonensis (AB626855), Tribolodon sachalinensis (AB626856), Tribolodon nakamurai (AB218896), Tribolodon brandtii (AB626853), Rhynchocypris kumgangensis (JQ675733), Rhodeus sericeus (KM052222; in this study), and Rhodeus lighti (NC_024885).
the sister taxon to Tribolodon was supported by bootstrap values of 49%. The five different geographical populations of the R. lagowskii formed a paraphyletic group with the high bootstrap value (45%) in all examinations.
Declaration of interest This research was supported by the Special Fund for Talent Cultivation From National Scientific Base for Basic Scientific Research and Teaching Talent Cultivation of Northeast Agricultural University in China (J1210069) and the Natural Science Foundation of Heilongjiang Province (QC2013C016).
References Campbell MA, Lo´pez JA, Satoh TP, Chen WJ, Miya M. (2014). Mitochondrial genomic investigation of flatfish monophyly. Gene 551: 176–82. Chen Y, Cheng QQ, Qiao HY, Zhu YX, Chen WM, Ren GJ. (2013). The complete mitochondrial genome sequence of Schizothorax wangchiachii (Cypriniformes: Cyprinidae). Mitochondrial DNA 24:353–5.
Hwang DS, Lee WO, Lee JS. (2014). Complete mitochondrial genome of the freshwater fish, Rhodeus suigensis (Cypriniformes, Cyprinidae). Mitochondrial DNA 25:5–6. Kim BC, Kang TW, Kim MS, Kim CB. (2006). The complete mitogenome of Rhodeus uyekii (Cypriniformes, Cyprinidae). DNA Sequence 17:181–6. Wei T, Zhang B, Sun YN. (2014). Structure comparison of control region in Stromateoidei and complete mitochondrial genome of the bluefin driftfish Psenes pellucidus (Perciformes, Nomeidae). Mitochondrial DNA 25:355–6. Xu W, Chen AH, Xia R, Fu CZ. (2014). Complete mitochondrial genome of Rhynchocypris cf. Lagowskii (Cypriniformes: Cyprinidae). Mitochondrial DNA 25:379–80. Yu JN, Kim S, Kwak M. (2014a). Complete mitochondrial genome sequence of a Korean Pungtungia herzi (Cypriniformes, Gobioninae). Mitochondrial DNA 25:414–15. Yu YY, Li YH, Wang WM, Zhou XY. (2014b). Complete mitochondrial genome of the natural triploid loach, Misgurnus anguillicaudatus (Teleostei: Cypriniformes: Cobitididae). Mitochondrial DNA 25: 353–4. Zhang HH, Xu CZ, Ma JZ. (2009). Structure of the mt DNA control region and phylogeny of the Mustelidae species. Acta Ecol Sin 29: 3585–92.
