Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Tanakia limbata (Cypriniformes: Cyprinidae) Yi Luo, Xiaojuan Cao & Yurong Zhu To cite this article: Yi Luo, Xiaojuan Cao & Yurong Zhu (2014): The complete mitochondrial genome of Tanakia limbata (Cypriniformes: Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.961135
Published online: 26 Sep 2014.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of California, San Diego]
Date: 08 November 2015, At: 07:21
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.961135
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Tanakia limbata (Cypriniformes: Cyprinidae) Yi Luo1,2,3, Xiaojuan Cao1,2,3, and Yurong Zhu1,2
Downloaded by [University of California, San Diego] at 07:21 08 November 2015
1
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, College of Fisheries, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China, 2Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China, and 3Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, Hubei, People’s Republic of China Abstract
Keywords
Bitterling Tanakia limbata is a temperate freshwater fish, distributes in fast-flowing creeks in central and southern Japan. In this study, the complete mitochondrial genome of T. limbata is sequenced to be 16,565 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, a control region and the origin of the light strand replication. The overall base composition of T. limbata in descending order is A 28.2%, C 27.5%, T 26.3%, and G 18.0%, with a slight A + T bias. The mitogenome sequence data may provide useful information to the population genetics analysis of T. limbata and the elucidation of evolutionary mechanisms in Cyprinidae.
Cyprinidae, mitochondrial genome, Tanakia limbata
Bitterling Tanakia limbata (Cypriniformes: Cyprinidae) is a temperate freshwater fish, belongs to subfamily Acheilognathinae, distributes in fast-flowing creeks in central and southern Japan. Because of its gorgeous color, T. limbata is being widely raised as ornamental fish in Japan. The comprehensive phylogenic analysis of subfamily Acheilognathinae are of importance in elucidating evolutionary adaptations in freshwater fishes in Asia. In addition, the phylogenetic relationships of bitterling are also expected to help to explore the coevolution between bitterling and freshwater mussel (Liu et al., 2006). However, unlike the other two bitterling genus Acheilognathus
History Received 27 August 2014 Accepted 31 August 2014 Published online 25 September 2014
and Rhodeus, the most complete mitochondrial genomes (mitogenomes) in Tanakia are still scarce (Saitoh et al., 2006; Yu et al., 2014). Herein, the complete mitochondrial genome (mitogenome) of T. limbata was sequenced with the aim of obtaining genetic information essential to inferring its evolution and genetic identity and phylogenetic analysis of Cyprinidae fish. Tanakia limbata were collected from Okayama-ken in Japan. Total genomic DNA from fin tissue was extracted using a modified ammonium acetate precipitation protocol (Nicholls et al., 2000). The mitogenome DNA (mtDNA) was isolated by long-polymerase chain reaction with two conserved primers and
Table 1. Characteristics of the mitochondrial genes of T. limbata. Position Gene tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn
From 1 69 1028 1100 2781 2857 3833 3973 3975 4044 5089 5229 5303
Codon To 68 1027 1099 2780 2856 3828 3904 3903 4043 5088 5159 5161 5231
Start
Stop*
ATG
TAG
ATG
T– –
Strand H H H H H H H L H H H L L
Intergenic nucleotide (bp)** 0 0 0 0 0 0 4 2 1 0 0 1 1 (continued )
Correspondence: Yurong Zhu, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China. Tel: +86-27 8728 2113. Fax: +86 27 8728 2114. E-mail: [email protected]
2
Y. Luo et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Downloaded by [University of California, San Diego] at 07:21 08 November 2015
Position
Codon
Gene
From
To
tRNA-Cys tRNA-Tyr COX1 tRNA-ser tRNA-Asp COX2 tRNA-Lys ATPase8 ATPase6 COX3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser tRNA-Leu ND5 ND6 tRNA-Glu CYTB tRNA-Thr tRNA-Pro D-loop
5401 5472 5474 7095 7098 7176 7867 7944 8102 8785 9569 9640 9989 10,059 10,349 11,731 11,800 11,870 11,943 14,296 14,365 14,371 15,512 15,654 15,655
5335 5402 7024 7025 7167 7866 7942 8108 8785 9568 9639 9990 10,058 10,355 11,729 11,799 11,868 11,942 13,778 13,775 14,297 15,511 15,585 15,585 16,565
Start
Stop*
GTG
TAA
ATG
T– –
ATG ATG ATG
TAA TAA T– –
ATG
TAG
ATG ATG
TAA T– –
ATG ATG
TAA TAG
ATG
T– –
Strand
Intergenic nucleotide (bp)**
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
31 0 1 0 2 8 0 1 7 1 0 0 2 0 7 1 0 1 0 4 0 5 0 1 0
*T– – represents incomplete stop codons; **Numbers correspond to the nucleotides separating adjacent genes. Negative numbers indicate overlapping nucleotides.
this mtDNA was sequenced by primer walking using flanking sequences as sequencing primers (Zhou et al., 2009). The PCR products were sent to Sangon Biotech Company (Shanghai, China) to be sequenced directly after purification. Sequences were assembled, and the mitogenome sequence of T. limbata had been deposited in the GenBank with accession number of KM386633. The T. limbata shares the same structural organization of mitogenome as many other fish species, like Acheilognathus somjinensis and Rhodeus uyekii (Hwang et al., 2014; Kim et al., 2006). The genome was 16,565 bp in length, and contains 22 transfer RNA genes, 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, a displacement loop region (D-loop) and the origin of the light strand replication (Table 1). Most of the mitochondrial genes of this species were encoded on heavy strand (H-strand) except for ND6 and eight tRNA genes, which were encoded on light strand (L-strand). The overall base composition of T. limbata in descending order was A 28.2%, C 27.5%, T 26.3%, and G 18.0%. The A + T and C + G contents of the mitogenome are 54.5% and 45.5%, respectively. All of the 13 PCGs contain the orthodox start codon ATG except COX1 that started with GTG. However, the end codons of the 13 PCGs varied with TAA, TAG or T (ND2, COX2, COX3, ND4 and CYTB). The control region (D-loop) was located between the tRNA-Pro and tRNA-Phe genes, and its length was 911 bp. The origin of light-strand replication (OL) extends up to 31 nucleotides and was identified between tRNA-Asn and tRNA-Cys. The mitogenomes from T. limbata and its congeneric species T. lanceolata have 88% nucleotide sequence identity (Xu et al., 2014).
Acknowledgements We thank Dr. Gao for collecting samples.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This study was supported by National Natural Science Foundation of China (31101647).
References Hwang DS, Byeon HK, Lee JS. (2014). Complete mitochondrial genome of the freshwater fish, Acheilognathus somjinensis (Cypriniformes, Cyprinidae). Mitochondrial DNA 25:13–14. Kim BC, Kang TW, Kim MS, Kim CB. (2006). The complete mitogenome of Rhodeus uyekii (Cypriniformes, Cyprinidae). DNA Seq 17:181–6. Liu H, Zhu Y, Smith C, Reichard M. (2006). Evidence of host specificity and congruence between phylogenies of bitterlings and freshwater mussels. Zool Stud 45:428–34. Nicholls JA, Double MC, Rowell DM, Magrath D. (2000). The evolution of cooperative and pair breeding in thornbills Acanthiza (Pardalotidae). J Avian Biol 31:165–76. Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, Nishida M, Miya M. (2006). Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63:826–41. Xu X, Chao X, Zhu Y. (2014). The complete mitochondrial genome of Tanakia lanceolata (Cypriniformes: Cyprinidae). Mitochondr DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.919480. Yu Y, Yi W, Ma Z, Yang R, Shen J. (2014). The complete mitochondrial genome of Rhodeus fangi (Cypriniformes, Cyprinidae, Acheilognathinae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/ 19401736.2014.892079. Zhou Z, Huang Y, Shi F, Ye H. (2009). The complete mitochondrial genome of Deracantha onos (Orthoptera: Bradyporidae). Mol Biol Rep 36:7–12.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Tanakia limbata (Cypriniformes: Cyprinidae) Yi Luo, Xiaojuan Cao & Yurong Zhu To cite this article: Yi Luo, Xiaojuan Cao & Yurong Zhu (2014): The complete mitochondrial genome of Tanakia limbata (Cypriniformes: Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.961135
Published online: 26 Sep 2014.
Submit your article to this journal
Article views: 7
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of California, San Diego]
Date: 08 November 2015, At: 07:21
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.961135
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Tanakia limbata (Cypriniformes: Cyprinidae) Yi Luo1,2,3, Xiaojuan Cao1,2,3, and Yurong Zhu1,2
Downloaded by [University of California, San Diego] at 07:21 08 November 2015
1
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, College of Fisheries, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China, 2Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China, and 3Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, Hubei, People’s Republic of China Abstract
Keywords
Bitterling Tanakia limbata is a temperate freshwater fish, distributes in fast-flowing creeks in central and southern Japan. In this study, the complete mitochondrial genome of T. limbata is sequenced to be 16,565 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, a control region and the origin of the light strand replication. The overall base composition of T. limbata in descending order is A 28.2%, C 27.5%, T 26.3%, and G 18.0%, with a slight A + T bias. The mitogenome sequence data may provide useful information to the population genetics analysis of T. limbata and the elucidation of evolutionary mechanisms in Cyprinidae.
Cyprinidae, mitochondrial genome, Tanakia limbata
Bitterling Tanakia limbata (Cypriniformes: Cyprinidae) is a temperate freshwater fish, belongs to subfamily Acheilognathinae, distributes in fast-flowing creeks in central and southern Japan. Because of its gorgeous color, T. limbata is being widely raised as ornamental fish in Japan. The comprehensive phylogenic analysis of subfamily Acheilognathinae are of importance in elucidating evolutionary adaptations in freshwater fishes in Asia. In addition, the phylogenetic relationships of bitterling are also expected to help to explore the coevolution between bitterling and freshwater mussel (Liu et al., 2006). However, unlike the other two bitterling genus Acheilognathus
History Received 27 August 2014 Accepted 31 August 2014 Published online 25 September 2014
and Rhodeus, the most complete mitochondrial genomes (mitogenomes) in Tanakia are still scarce (Saitoh et al., 2006; Yu et al., 2014). Herein, the complete mitochondrial genome (mitogenome) of T. limbata was sequenced with the aim of obtaining genetic information essential to inferring its evolution and genetic identity and phylogenetic analysis of Cyprinidae fish. Tanakia limbata were collected from Okayama-ken in Japan. Total genomic DNA from fin tissue was extracted using a modified ammonium acetate precipitation protocol (Nicholls et al., 2000). The mitogenome DNA (mtDNA) was isolated by long-polymerase chain reaction with two conserved primers and
Table 1. Characteristics of the mitochondrial genes of T. limbata. Position Gene tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn
From 1 69 1028 1100 2781 2857 3833 3973 3975 4044 5089 5229 5303
Codon To 68 1027 1099 2780 2856 3828 3904 3903 4043 5088 5159 5161 5231
Start
Stop*
ATG
TAG
ATG
T– –
Strand H H H H H H H L H H H L L
Intergenic nucleotide (bp)** 0 0 0 0 0 0 4 2 1 0 0 1 1 (continued )
Correspondence: Yurong Zhu, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China. Tel: +86-27 8728 2113. Fax: +86 27 8728 2114. E-mail: [email protected]
2
Y. Luo et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Downloaded by [University of California, San Diego] at 07:21 08 November 2015
Position
Codon
Gene
From
To
tRNA-Cys tRNA-Tyr COX1 tRNA-ser tRNA-Asp COX2 tRNA-Lys ATPase8 ATPase6 COX3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser tRNA-Leu ND5 ND6 tRNA-Glu CYTB tRNA-Thr tRNA-Pro D-loop
5401 5472 5474 7095 7098 7176 7867 7944 8102 8785 9569 9640 9989 10,059 10,349 11,731 11,800 11,870 11,943 14,296 14,365 14,371 15,512 15,654 15,655
5335 5402 7024 7025 7167 7866 7942 8108 8785 9568 9639 9990 10,058 10,355 11,729 11,799 11,868 11,942 13,778 13,775 14,297 15,511 15,585 15,585 16,565
Start
Stop*
GTG
TAA
ATG
T– –
ATG ATG ATG
TAA TAA T– –
ATG
TAG
ATG ATG
TAA T– –
ATG ATG
TAA TAG
ATG
T– –
Strand
Intergenic nucleotide (bp)**
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
31 0 1 0 2 8 0 1 7 1 0 0 2 0 7 1 0 1 0 4 0 5 0 1 0
*T– – represents incomplete stop codons; **Numbers correspond to the nucleotides separating adjacent genes. Negative numbers indicate overlapping nucleotides.
this mtDNA was sequenced by primer walking using flanking sequences as sequencing primers (Zhou et al., 2009). The PCR products were sent to Sangon Biotech Company (Shanghai, China) to be sequenced directly after purification. Sequences were assembled, and the mitogenome sequence of T. limbata had been deposited in the GenBank with accession number of KM386633. The T. limbata shares the same structural organization of mitogenome as many other fish species, like Acheilognathus somjinensis and Rhodeus uyekii (Hwang et al., 2014; Kim et al., 2006). The genome was 16,565 bp in length, and contains 22 transfer RNA genes, 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, a displacement loop region (D-loop) and the origin of the light strand replication (Table 1). Most of the mitochondrial genes of this species were encoded on heavy strand (H-strand) except for ND6 and eight tRNA genes, which were encoded on light strand (L-strand). The overall base composition of T. limbata in descending order was A 28.2%, C 27.5%, T 26.3%, and G 18.0%. The A + T and C + G contents of the mitogenome are 54.5% and 45.5%, respectively. All of the 13 PCGs contain the orthodox start codon ATG except COX1 that started with GTG. However, the end codons of the 13 PCGs varied with TAA, TAG or T (ND2, COX2, COX3, ND4 and CYTB). The control region (D-loop) was located between the tRNA-Pro and tRNA-Phe genes, and its length was 911 bp. The origin of light-strand replication (OL) extends up to 31 nucleotides and was identified between tRNA-Asn and tRNA-Cys. The mitogenomes from T. limbata and its congeneric species T. lanceolata have 88% nucleotide sequence identity (Xu et al., 2014).
Acknowledgements We thank Dr. Gao for collecting samples.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This study was supported by National Natural Science Foundation of China (31101647).
References Hwang DS, Byeon HK, Lee JS. (2014). Complete mitochondrial genome of the freshwater fish, Acheilognathus somjinensis (Cypriniformes, Cyprinidae). Mitochondrial DNA 25:13–14. Kim BC, Kang TW, Kim MS, Kim CB. (2006). The complete mitogenome of Rhodeus uyekii (Cypriniformes, Cyprinidae). DNA Seq 17:181–6. Liu H, Zhu Y, Smith C, Reichard M. (2006). Evidence of host specificity and congruence between phylogenies of bitterlings and freshwater mussels. Zool Stud 45:428–34. Nicholls JA, Double MC, Rowell DM, Magrath D. (2000). The evolution of cooperative and pair breeding in thornbills Acanthiza (Pardalotidae). J Avian Biol 31:165–76. Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, Nishida M, Miya M. (2006). Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63:826–41. Xu X, Chao X, Zhu Y. (2014). The complete mitochondrial genome of Tanakia lanceolata (Cypriniformes: Cyprinidae). Mitochondr DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.919480. Yu Y, Yi W, Ma Z, Yang R, Shen J. (2014). The complete mitochondrial genome of Rhodeus fangi (Cypriniformes, Cyprinidae, Acheilognathinae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/ 19401736.2014.892079. Zhou Z, Huang Y, Shi F, Ye H. (2009). The complete mitochondrial genome of Deracantha onos (Orthoptera: Bradyporidae). Mol Biol Rep 36:7–12.
