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
New complete mitochondrial genome of the Odontobutis potamophila (Perciformes, Odontobutidae): genome description and phylogenetic performance Qiang Li & Zhizhi Liu To cite this article: Qiang Li & Zhizhi Liu (2014): New complete mitochondrial genome of the Odontobutis potamophila (Perciformes, Odontobutidae): genome description and phylogenetic performance, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2013.878925
Published online: 22 Jan 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 Santa Barbara]
Date: 06 November 2015, At: 06:57
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.878925
MITOGENOME ANNOUNCEMENT
New complete mitochondrial genome of the Odontobutis potamophila (Perciformes, Odontobutidae): genome description and phylogenetic performance
Downloaded by [University of California Santa Barbara] at 06:57 06 November 2015
Qiang Li and Zhizhi Liu Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, P.R. China Abstract
Keywords
A new complete sequence of mitochondrial genome of Odontobutis potamophila has been reported. It was 16,843 bp and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. Except for 8 tRNA and ND6 genes, all other mitochondrial genes were encoded on the heavy strand. Phylogenetic comparison proved that ND4, ND5 and ND6 genes might be dependable ‘‘leading’’ indicators of lineage divergence in Odontobutis obscurus. Also, COII, ND5 and cytb genes are useful in examining intraspecific population genetic diversity.
Mitogenome, Odontobutis potamophila, phylogenetic performance
The Odontobutis potamophila (Perciformes, Odontobutidae), is a small benthic freshwater goby and promising aquaculture fish during recent years in China. Because of similar phenotypes, it was mistaken for O. obscura for a long time, which only districted in Japan. In 1993, the two species were finally separated via sense hole C at back of eyes (Wu et al., 1993). Though, in 2013, the complete mitogenome of O. platycephala (NC010199.1) could be obtained from GenBank, there are still rare studies on its genetic resources since then (Ren & Zhang, 2007). Here, in order to compare the difference between individuals of O. potamophila and phylogenetic performance among Odontobutis by mitogenome, we obtained a new complete one. The sample was collected from Yangtze River Estuary. Three PCR primers were initially obtained from Liu et al. (2012), and
History Received 18 December 2013 Accepted 18 December 2013 Published online 22 January 2014
the other three were designed according to COI (DQ010651), Cytb (KC292213) and control region (AP004454) sequences from GenBank. Subsequently, based on the received sequences, five additional primers were designed to supplement residual gaps. Finally, DNA Baser V3.5.4 (http://www.dnabaser.com/ news/index.html) was used to sequence analysis and assembly. The new complete mitochondrial genome of O. potamophila was 16,843 bp in length (KF874495) and had a 330 bp gap between tRNALeu and tRNAHis like the reported sequences of O. platycephala, O. potamophila (KF305680) and O. sinensis (KF154120.1). Mitogenome database were annotated by MitoFish (Iwasaki et al., 2013). It was composed of 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and a putative control region (Table 1). All genes were encoded on the heavy strand besides ND6 and 8 tRNA. For protein-coding genes, 11 were
Table 1. The characteristics of mitochondrial genome of O. potamophila. Gene Phe
tRNA 12S-rRNA tRNAVal 16S-rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp
Position
Size (bp)
1–69 70–1022 1023–1094 1095–2756 2757–2829 2830–3808 3809–3878 3878–3948 3948–4016 4018–5059 5060–5132
69 953 72 1662 73 979 70 71 69 1042 73
Start codon
Stop codon
Anti codon GAA TAC TAA
ATG
TA GAT TTG CAT
ATG
TA TCA
Intergenic nucleotid* 0 0 0 0 0 0 1 1 1 0 6
Strand+ H H H H H H H L H H H (continued )
Correspondence: Zhizhi Liu, Key laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, P.R. China. Tel: +86 21 61900425. Fax: +86 21 61900425. E-mail: [email protected]
2
Q. Li & Z. Liu
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Gene
Downloaded by [University of California Santa Barbara] at 06:57 06 November 2015
Ala
tRNA tRNAAsn tRNACys tRNATyr COI tRNASer tRNAAsp COII tRNALys ATP8 ATP6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNASer tRNALeu tRNAHis ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro CR
Position
Size (bp)
5139–5207 5209–5281 5316–5382 5383–5450 5452–7005 7006–7077 7081–7151 7157–7746 7747–7820 7822–7986 7980–8620 8619–9454 9455–9525 9526–9873 9874–9942 9943–10,239 10,233–11,617 11,659–11,726 11,730–11,801 12,134–12,201 12,206–14,113 14,114–14,637 14,636–14,703 14,708–15,850 15,851–15,922 15,925–15,994 15,995–16,843
69 73 67 68 1554 72 71 590 74 165 641 836 71 347 69 297 1385 68 72 68 1908 524 68 1143 72 70 849
Start codon
GTG
Stop codon
Anti codon
Intergenic nucleotid*
Strand+
TGC GTT GCA GTA
1 34 0 1 0 3 5 0 1 7 2 0 0 0 0 6 41 3 332 4 0 2 16 0 2 0 0
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
TAA TGA GTC
ATG
T
ATG ATA ATG
TAA TAA TA
ATG
T
ATG ATG
TAA TAA
TTT
TCC TCG GCT TAG GTG ATG ATG
TAA TAA
ATG
T
TTC TGT TGG
*Positive numbers indicate the number of nucleotides found in intergenic spacers between different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. +H and L indicate genes transcribed on the heavy and light strands, respectively.
initiated with the orthodox ATG except for COI with GTG, and they had 3 types of stop codons (TAA, TA– and T–). All tRNAs were recognized by tRNAscan-SE1.21 (Lowe & Eddy, 1997), and their length ranged from 67 to 73 bp. The 2 rRNA genes were typically located as other species. Unlike O. platycephala and O. sinensis, including a pointless 4–13 tandem repeats, the control region did not have any repeats even in 10 individuals. The content A + T(55.3%) was higher than the G + C content, which was similar to mudskipper’s (Liu et al., 2012). The differences of four mitogenome sequences mainly existed in the protein-coding genes, with 0.09–7.19% variation in O. potamophila and 20.22–35.56% range among the three Odontobutis species. Phylogenetic comparison proved that ND4, ND5 and ND6 genes might be dependable ‘‘leading’’ indicators of lineage divergence in Odontobutis obscurus, and COII, ND5 and cytb genes could be used to examine population genetic diversity at the intraspecific level (Makay et al., 2013; Zardoya & Meyer, 1996).
Acknowledgements The authors would like to thank Miss Tianrui Zhang and Liwei Su for their helpful suggestions during the period of study.
Declaration of interest The authors report no conflict of interest. The authors alone are responsible for the content and writing of the paper. This work was
funded by Shanghai Outstanding Undergraduate Scholarship for Interdisciplinary Training, and Shanghai University First-class Disciplines Project of Fishries.
References Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, et al. (2013). MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol 30:2531–40. Liu ZZ, Wang CT, Ma LB, He AY, Yang JQ, Tang WQ. (2012). Complete mitochondrial genome of the mudskipper Boleophthalmus pectinirostr is (Perciformes, Gobiidae): Repetitive sequences in the control region. Mitochondrial DNA 23:31–3. Lowe TM, Eddy SR. (1997). tRNA scan-SE 1.21: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–64. Makay BD, Maysjr HL, Wu YCH, Li H, Yao CHT, Nishiumi I, Zou FSH. (2013). An empirical comparison of character-based and coalescentbased approaches to species delimitation in a young avian complex. Mol Ecol 22:4943–57. Ren G, Zhang Q. (2007). Molecular phylogeny of the genus Odontobutis based upon partial sequences of mitochondrial 12S rRNA genes. Acta Hydrobiol Sin 31:473–8. Wu HL, Wu XQ, Xie YH. (1993). A revision of the genus Odontobutis from China with description of a new species. J Shanghai Fish Univ 1: 52–61. Zardoya R, Meyer A. (1996). Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol Biol Evol 13:933–42.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
New complete mitochondrial genome of the Odontobutis potamophila (Perciformes, Odontobutidae): genome description and phylogenetic performance Qiang Li & Zhizhi Liu To cite this article: Qiang Li & Zhizhi Liu (2014): New complete mitochondrial genome of the Odontobutis potamophila (Perciformes, Odontobutidae): genome description and phylogenetic performance, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2013.878925
Published online: 22 Jan 2014.
Submit your article to this journal
Article views: 12
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 Santa Barbara]
Date: 06 November 2015, At: 06:57
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.878925
MITOGENOME ANNOUNCEMENT
New complete mitochondrial genome of the Odontobutis potamophila (Perciformes, Odontobutidae): genome description and phylogenetic performance
Downloaded by [University of California Santa Barbara] at 06:57 06 November 2015
Qiang Li and Zhizhi Liu Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, P.R. China Abstract
Keywords
A new complete sequence of mitochondrial genome of Odontobutis potamophila has been reported. It was 16,843 bp and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. Except for 8 tRNA and ND6 genes, all other mitochondrial genes were encoded on the heavy strand. Phylogenetic comparison proved that ND4, ND5 and ND6 genes might be dependable ‘‘leading’’ indicators of lineage divergence in Odontobutis obscurus. Also, COII, ND5 and cytb genes are useful in examining intraspecific population genetic diversity.
Mitogenome, Odontobutis potamophila, phylogenetic performance
The Odontobutis potamophila (Perciformes, Odontobutidae), is a small benthic freshwater goby and promising aquaculture fish during recent years in China. Because of similar phenotypes, it was mistaken for O. obscura for a long time, which only districted in Japan. In 1993, the two species were finally separated via sense hole C at back of eyes (Wu et al., 1993). Though, in 2013, the complete mitogenome of O. platycephala (NC010199.1) could be obtained from GenBank, there are still rare studies on its genetic resources since then (Ren & Zhang, 2007). Here, in order to compare the difference between individuals of O. potamophila and phylogenetic performance among Odontobutis by mitogenome, we obtained a new complete one. The sample was collected from Yangtze River Estuary. Three PCR primers were initially obtained from Liu et al. (2012), and
History Received 18 December 2013 Accepted 18 December 2013 Published online 22 January 2014
the other three were designed according to COI (DQ010651), Cytb (KC292213) and control region (AP004454) sequences from GenBank. Subsequently, based on the received sequences, five additional primers were designed to supplement residual gaps. Finally, DNA Baser V3.5.4 (http://www.dnabaser.com/ news/index.html) was used to sequence analysis and assembly. The new complete mitochondrial genome of O. potamophila was 16,843 bp in length (KF874495) and had a 330 bp gap between tRNALeu and tRNAHis like the reported sequences of O. platycephala, O. potamophila (KF305680) and O. sinensis (KF154120.1). Mitogenome database were annotated by MitoFish (Iwasaki et al., 2013). It was composed of 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and a putative control region (Table 1). All genes were encoded on the heavy strand besides ND6 and 8 tRNA. For protein-coding genes, 11 were
Table 1. The characteristics of mitochondrial genome of O. potamophila. Gene Phe
tRNA 12S-rRNA tRNAVal 16S-rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp
Position
Size (bp)
1–69 70–1022 1023–1094 1095–2756 2757–2829 2830–3808 3809–3878 3878–3948 3948–4016 4018–5059 5060–5132
69 953 72 1662 73 979 70 71 69 1042 73
Start codon
Stop codon
Anti codon GAA TAC TAA
ATG
TA GAT TTG CAT
ATG
TA TCA
Intergenic nucleotid* 0 0 0 0 0 0 1 1 1 0 6
Strand+ H H H H H H H L H H H (continued )
Correspondence: Zhizhi Liu, Key laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, P.R. China. Tel: +86 21 61900425. Fax: +86 21 61900425. E-mail: [email protected]
2
Q. Li & Z. Liu
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Gene
Downloaded by [University of California Santa Barbara] at 06:57 06 November 2015
Ala
tRNA tRNAAsn tRNACys tRNATyr COI tRNASer tRNAAsp COII tRNALys ATP8 ATP6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNASer tRNALeu tRNAHis ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro CR
Position
Size (bp)
5139–5207 5209–5281 5316–5382 5383–5450 5452–7005 7006–7077 7081–7151 7157–7746 7747–7820 7822–7986 7980–8620 8619–9454 9455–9525 9526–9873 9874–9942 9943–10,239 10,233–11,617 11,659–11,726 11,730–11,801 12,134–12,201 12,206–14,113 14,114–14,637 14,636–14,703 14,708–15,850 15,851–15,922 15,925–15,994 15,995–16,843
69 73 67 68 1554 72 71 590 74 165 641 836 71 347 69 297 1385 68 72 68 1908 524 68 1143 72 70 849
Start codon
GTG
Stop codon
Anti codon
Intergenic nucleotid*
Strand+
TGC GTT GCA GTA
1 34 0 1 0 3 5 0 1 7 2 0 0 0 0 6 41 3 332 4 0 2 16 0 2 0 0
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
TAA TGA GTC
ATG
T
ATG ATA ATG
TAA TAA TA
ATG
T
ATG ATG
TAA TAA
TTT
TCC TCG GCT TAG GTG ATG ATG
TAA TAA
ATG
T
TTC TGT TGG
*Positive numbers indicate the number of nucleotides found in intergenic spacers between different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. +H and L indicate genes transcribed on the heavy and light strands, respectively.
initiated with the orthodox ATG except for COI with GTG, and they had 3 types of stop codons (TAA, TA– and T–). All tRNAs were recognized by tRNAscan-SE1.21 (Lowe & Eddy, 1997), and their length ranged from 67 to 73 bp. The 2 rRNA genes were typically located as other species. Unlike O. platycephala and O. sinensis, including a pointless 4–13 tandem repeats, the control region did not have any repeats even in 10 individuals. The content A + T(55.3%) was higher than the G + C content, which was similar to mudskipper’s (Liu et al., 2012). The differences of four mitogenome sequences mainly existed in the protein-coding genes, with 0.09–7.19% variation in O. potamophila and 20.22–35.56% range among the three Odontobutis species. Phylogenetic comparison proved that ND4, ND5 and ND6 genes might be dependable ‘‘leading’’ indicators of lineage divergence in Odontobutis obscurus, and COII, ND5 and cytb genes could be used to examine population genetic diversity at the intraspecific level (Makay et al., 2013; Zardoya & Meyer, 1996).
Acknowledgements The authors would like to thank Miss Tianrui Zhang and Liwei Su for their helpful suggestions during the period of study.
Declaration of interest The authors report no conflict of interest. The authors alone are responsible for the content and writing of the paper. This work was
funded by Shanghai Outstanding Undergraduate Scholarship for Interdisciplinary Training, and Shanghai University First-class Disciplines Project of Fishries.
References Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, et al. (2013). MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol 30:2531–40. Liu ZZ, Wang CT, Ma LB, He AY, Yang JQ, Tang WQ. (2012). Complete mitochondrial genome of the mudskipper Boleophthalmus pectinirostr is (Perciformes, Gobiidae): Repetitive sequences in the control region. Mitochondrial DNA 23:31–3. Lowe TM, Eddy SR. (1997). tRNA scan-SE 1.21: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–64. Makay BD, Maysjr HL, Wu YCH, Li H, Yao CHT, Nishiumi I, Zou FSH. (2013). An empirical comparison of character-based and coalescentbased approaches to species delimitation in a young avian complex. Mol Ecol 22:4943–57. Ren G, Zhang Q. (2007). Molecular phylogeny of the genus Odontobutis based upon partial sequences of mitochondrial 12S rRNA genes. Acta Hydrobiol Sin 31:473–8. Wu HL, Wu XQ, Xie YH. (1993). A revision of the genus Odontobutis from China with description of a new species. J Shanghai Fish Univ 1: 52–61. Zardoya R, Meyer A. (1996). Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol Biol Evol 13:933–42.
