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 Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae) Peng Xie, Mengjun Ao, Chengjie Liu, Zhiming Zhang, Yun Zhang, Jiangong Niu, Adahbek Karjan & Xufa Ma To cite this article: Peng Xie, Mengjun Ao, Chengjie Liu, Zhiming Zhang, Yun Zhang, Jiangong Niu, Adahbek Karjan & Xufa Ma (2014): The complete mitochondrial genome of Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.880893
Published online: 18 Feb 2014.
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Date: 05 November 2015, At: 14:06
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.880893
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae) Peng Xie1, Mengjun Ao1, Chengjie Liu1, Zhiming Zhang1, Yun Zhang1, Jiangong Niu2, Adahbek Karjan2, and Xufa Ma1 College of Fisheries, Huazhong Agricultural University, Wuhan, China and 2Xinjiang Fisheries Research Institute, Urumqi, China
Downloaded by [Deakin University Library] at 14:06 05 November 2015
1
Abstract
Keywords
As reported, previous studies of Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae) have focused primarily on morphology and ecology. In this study, we cloned and sequenced the complete nucleotide sequence of the mitochondrial genome for P. phoxinus ujmonensis. The mitogenome was 17,738 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition of the heavy strain was 28.50% for A, 28.24% for T, 25.32% for C and 17.94% for G. The control region was revealed to contain tandem repeats. The mitogenome data of P. phoxinus ujmonensis should contribute to phylogenetic analysis and studies of population genetics of Phoxinus fishes.
Control region, mitochondrial genome, Phoxinus phoxinus ujmonensis
Phoxinus phoxinus ujmonensis, a small cold freshwater fish, is mainly distributed in Irtysh River in Northwest China (Ren et al., 2002). In the past, the genetic characteristics of the subfamily Phoxinus have come under investigation by means of molecular markers (Collin & Fumagalli, 2011; Imoto et al., 2012; Saitoh et al., 2006), but the phylogenetic position of Phoxinus is rather ambiguous. In this study, we reported the complete mitochondrial genome (mitogenome) of P. phoxinus ujmonensis, and hoped that it could play important roles in the studies of phylogenetic analysis and population genetics of this species. The P. phoxinus ujmonensis samples were collected in the lower stream of the Irtysh River, which is a cross-border river of China and Kazakhstan, in 2013. Total genomic DNA from fin tissue was extracted using a modified ammonium acetate
History Received 29 December 2013 Accepted 5 January 2014 Published online 18 February 2014
precipitation protocol (Li et al., 2011). In order to amplify the whole mitogenome sequence, we designed twenty-five pairs of PCR primers, which were based on the conserved sequences from the related species P. phoxinus, available in GenBank. The mitochondrial genome of P. phoxinus ujmonensis (GenBank accession number of KJ000673) was a circular molecule of 17,738 nucleotides. Compared with P. phoxinus, the mitogenome of P. phoxinus ujmonensis has a mostly conserved structural organization: it contains 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA (12S rRNA and 16S rRNA) genes, and 2 main noncoding regions (the control region (CR) and the origin of the light strand replication (OL)). As shown in Table 1, most of the mitochondrial genes were encoded on the H-strand, although the ND6 gene and
Table 1. Characteristics of the mitochondrial genes of P. phoxinus ujmonensis. Position Gene name tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp
From 1 70 1027 1099 2791 2868 3847 3917 3989 4058 5103
Codon To 69 1026 1098 2790 2867 3842 3918 3987 4057 5104 5173
Size (bp) 69 957 72 1692 77 975 72 71 69 1047 71
Stopa
Strand
ATG
TAG
ATG
TAG
H H H H H H H L H H H
Start
Intergenic nucleotide (bp)b 0 0 0 0 0 0 4 2 1 0 2 (continued )
Correspondence: Xufa Ma, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China. Tel: +86 2787282113. Fax: +86 2787282114. E-mail: [email protected]
2
P. Xie et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Downloaded by [Deakin University Library] at 14:06 05 November 2015
Position
Codon
Gene name
From
To
Size (bp)
tRNA-Ala tRNA-Asn tRNA-Cys tRNA-Tyr COX1 tRNA-ser tRNA-Asp COX2 tRNA-Lys ATP8 ATP6 COX3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser tRNA-Leu ND5 ND6 tRNA-Glu Cyt b tRNA-Thr tRNA-Pro Control region
5175 5245 5349 5418 5490 7041 7114 7202 7893 7970 8128 8811 9595 9666 10,015 10,084 10,374 11,756 11,825 11,895 11,968 13,800 14,322 14,396 15,537 15,608 15,678
5243 5317 5416 5488 7040 7111 7187 7892 7968 8134 8811 9595 9665 10,016 10,083 10,380 11,756 11,824 11,893 11,967 13,803 14,321 14,390 15,536 15,608 15,677 17,738
69 73 68 71 1551 71 74 691 76 165 684 785 71 351 69 297 1383 69 69 73 1836 522 69 1141 72 70 2061
Start
Stopa
GTG
TAA
ATG
T– –
ATG ATG ATG
TAG TAA TA–
GTG
TAG
ATG ATG
TAA TAG
ATG ATG
TAA TAG
ATG
T– –
Strand
Intergenic nucleotide (bp)b
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
1 1 31 1 1 0 2 14 0 1 7 1 1 0 2 0 7 1 0 1 0 4 0 5 0 1 0
Negative numbers indicate overlapping nucleotides. a T– – represents incomplete stop codon. b Numbers correspond to the nucleotides separating adjacent genes.
eight tRNA genes were encoded on the L-strand. The largest noncoding region was located between the tRNA-Pro and tRNA-Phe genes and was 2061 bp in length. The second non-coding sequence is the origin of light-strand replication, which extends up to 31 nucleotides. It was located in a cluster of five tRNA genes (the WANCY region) between tRNA-Asn and tRNA-Cys gene. Eleven PCGs of P. phoxinus ujmonensis shared the orthodox start codon ATG, while COX1 and ND3 began with GTG. However, the end codons of the 13 PCGs varied with TAA, TA, T or TAG, and the incomplete stop codons were presumably completed by posttranscriptional polyadenylation (Ojala et al., 1981). The sequence overlaps among 13 protein-coding genes are shown in Table 1. The highest level of DNA sequence overlaps of P. phoxinus ujmonensis was found on ATP8-ATP6, ND4-ND4L, and ND5-ND6, and they overlapped by seven, seven, and four nucleotides, respectively. A number of other genes shared one or two nucleotides in common with adjacent tRNA genes. The 22 deduced tRNA genes ranged in size from 68 to 77 bp with a total length of 1565 bp. The 12S and 16S ribosomal RNA genes contain 957 bp and 1692 bp, respectively. These two rRNA genes were located between tRNA-Phe and tRNA-Leu (UUR), and are separated by tRNA-Val.
Declaration of interest This work was financially supported by the Special Funds for the Foundation Work of Science and Technology (No. 2012FY112700).
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Collin H, Fumagalli L. (2011). Evidence for morphological and adaptive genetic divergence between lake and stream habitats in European minnows (Phoxinus phoxinus, Cyprinidae). Mol Ecol 20: 4490–502. Imoto JM, Saitoh K, Sasaki T, Yonezawa T, Adachi J, Kartavtsev YP, Miya M, et al. (2012). Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis. Gene 514: 112–24. Li Y, Wang W, Liu X, Luo W, Zhang J, Yasmeen JG. (2011). DNA extraction from crayfish exoskeleton. Indian J Exp Biol 49: 953–7. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Ren M, Guo Y, Zhang R, Zhang X, Cai L, Li H, Adahbek K, et al. (2002). Fish resources and fisheries of Irtysh River, China. Urumqi, China: Xinjiang Science, Technology and Sanitation Publishing House. p 88–93 (in Chinese). 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.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae) Peng Xie, Mengjun Ao, Chengjie Liu, Zhiming Zhang, Yun Zhang, Jiangong Niu, Adahbek Karjan & Xufa Ma To cite this article: Peng Xie, Mengjun Ao, Chengjie Liu, Zhiming Zhang, Yun Zhang, Jiangong Niu, Adahbek Karjan & Xufa Ma (2014): The complete mitochondrial genome of Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.880893
Published online: 18 Feb 2014.
Submit your article to this journal
Article views: 28
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: [Deakin University Library]
Date: 05 November 2015, At: 14:06
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.880893
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae) Peng Xie1, Mengjun Ao1, Chengjie Liu1, Zhiming Zhang1, Yun Zhang1, Jiangong Niu2, Adahbek Karjan2, and Xufa Ma1 College of Fisheries, Huazhong Agricultural University, Wuhan, China and 2Xinjiang Fisheries Research Institute, Urumqi, China
Downloaded by [Deakin University Library] at 14:06 05 November 2015
1
Abstract
Keywords
As reported, previous studies of Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae) have focused primarily on morphology and ecology. In this study, we cloned and sequenced the complete nucleotide sequence of the mitochondrial genome for P. phoxinus ujmonensis. The mitogenome was 17,738 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition of the heavy strain was 28.50% for A, 28.24% for T, 25.32% for C and 17.94% for G. The control region was revealed to contain tandem repeats. The mitogenome data of P. phoxinus ujmonensis should contribute to phylogenetic analysis and studies of population genetics of Phoxinus fishes.
Control region, mitochondrial genome, Phoxinus phoxinus ujmonensis
Phoxinus phoxinus ujmonensis, a small cold freshwater fish, is mainly distributed in Irtysh River in Northwest China (Ren et al., 2002). In the past, the genetic characteristics of the subfamily Phoxinus have come under investigation by means of molecular markers (Collin & Fumagalli, 2011; Imoto et al., 2012; Saitoh et al., 2006), but the phylogenetic position of Phoxinus is rather ambiguous. In this study, we reported the complete mitochondrial genome (mitogenome) of P. phoxinus ujmonensis, and hoped that it could play important roles in the studies of phylogenetic analysis and population genetics of this species. The P. phoxinus ujmonensis samples were collected in the lower stream of the Irtysh River, which is a cross-border river of China and Kazakhstan, in 2013. Total genomic DNA from fin tissue was extracted using a modified ammonium acetate
History Received 29 December 2013 Accepted 5 January 2014 Published online 18 February 2014
precipitation protocol (Li et al., 2011). In order to amplify the whole mitogenome sequence, we designed twenty-five pairs of PCR primers, which were based on the conserved sequences from the related species P. phoxinus, available in GenBank. The mitochondrial genome of P. phoxinus ujmonensis (GenBank accession number of KJ000673) was a circular molecule of 17,738 nucleotides. Compared with P. phoxinus, the mitogenome of P. phoxinus ujmonensis has a mostly conserved structural organization: it contains 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA (12S rRNA and 16S rRNA) genes, and 2 main noncoding regions (the control region (CR) and the origin of the light strand replication (OL)). As shown in Table 1, most of the mitochondrial genes were encoded on the H-strand, although the ND6 gene and
Table 1. Characteristics of the mitochondrial genes of P. phoxinus ujmonensis. Position Gene name tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp
From 1 70 1027 1099 2791 2868 3847 3917 3989 4058 5103
Codon To 69 1026 1098 2790 2867 3842 3918 3987 4057 5104 5173
Size (bp) 69 957 72 1692 77 975 72 71 69 1047 71
Stopa
Strand
ATG
TAG
ATG
TAG
H H H H H H H L H H H
Start
Intergenic nucleotide (bp)b 0 0 0 0 0 0 4 2 1 0 2 (continued )
Correspondence: Xufa Ma, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China. Tel: +86 2787282113. Fax: +86 2787282114. E-mail: [email protected]
2
P. Xie et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Downloaded by [Deakin University Library] at 14:06 05 November 2015
Position
Codon
Gene name
From
To
Size (bp)
tRNA-Ala tRNA-Asn tRNA-Cys tRNA-Tyr COX1 tRNA-ser tRNA-Asp COX2 tRNA-Lys ATP8 ATP6 COX3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser tRNA-Leu ND5 ND6 tRNA-Glu Cyt b tRNA-Thr tRNA-Pro Control region
5175 5245 5349 5418 5490 7041 7114 7202 7893 7970 8128 8811 9595 9666 10,015 10,084 10,374 11,756 11,825 11,895 11,968 13,800 14,322 14,396 15,537 15,608 15,678
5243 5317 5416 5488 7040 7111 7187 7892 7968 8134 8811 9595 9665 10,016 10,083 10,380 11,756 11,824 11,893 11,967 13,803 14,321 14,390 15,536 15,608 15,677 17,738
69 73 68 71 1551 71 74 691 76 165 684 785 71 351 69 297 1383 69 69 73 1836 522 69 1141 72 70 2061
Start
Stopa
GTG
TAA
ATG
T– –
ATG ATG ATG
TAG TAA TA–
GTG
TAG
ATG ATG
TAA TAG
ATG ATG
TAA TAG
ATG
T– –
Strand
Intergenic nucleotide (bp)b
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
1 1 31 1 1 0 2 14 0 1 7 1 1 0 2 0 7 1 0 1 0 4 0 5 0 1 0
Negative numbers indicate overlapping nucleotides. a T– – represents incomplete stop codon. b Numbers correspond to the nucleotides separating adjacent genes.
eight tRNA genes were encoded on the L-strand. The largest noncoding region was located between the tRNA-Pro and tRNA-Phe genes and was 2061 bp in length. The second non-coding sequence is the origin of light-strand replication, which extends up to 31 nucleotides. It was located in a cluster of five tRNA genes (the WANCY region) between tRNA-Asn and tRNA-Cys gene. Eleven PCGs of P. phoxinus ujmonensis shared the orthodox start codon ATG, while COX1 and ND3 began with GTG. However, the end codons of the 13 PCGs varied with TAA, TA, T or TAG, and the incomplete stop codons were presumably completed by posttranscriptional polyadenylation (Ojala et al., 1981). The sequence overlaps among 13 protein-coding genes are shown in Table 1. The highest level of DNA sequence overlaps of P. phoxinus ujmonensis was found on ATP8-ATP6, ND4-ND4L, and ND5-ND6, and they overlapped by seven, seven, and four nucleotides, respectively. A number of other genes shared one or two nucleotides in common with adjacent tRNA genes. The 22 deduced tRNA genes ranged in size from 68 to 77 bp with a total length of 1565 bp. The 12S and 16S ribosomal RNA genes contain 957 bp and 1692 bp, respectively. These two rRNA genes were located between tRNA-Phe and tRNA-Leu (UUR), and are separated by tRNA-Val.
Declaration of interest This work was financially supported by the Special Funds for the Foundation Work of Science and Technology (No. 2012FY112700).
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Collin H, Fumagalli L. (2011). Evidence for morphological and adaptive genetic divergence between lake and stream habitats in European minnows (Phoxinus phoxinus, Cyprinidae). Mol Ecol 20: 4490–502. Imoto JM, Saitoh K, Sasaki T, Yonezawa T, Adachi J, Kartavtsev YP, Miya M, et al. (2012). Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis. Gene 514: 112–24. Li Y, Wang W, Liu X, Luo W, Zhang J, Yasmeen JG. (2011). DNA extraction from crayfish exoskeleton. Indian J Exp Biol 49: 953–7. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Ren M, Guo Y, Zhang R, Zhang X, Cai L, Li H, Adahbek K, et al. (2002). Fish resources and fisheries of Irtysh River, China. Urumqi, China: Xinjiang Science, Technology and Sanitation Publishing House. p 88–93 (in Chinese). 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.
