http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1018205
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Gobiobotia filifer (Teleostei, Cypriniformes: Cyprinidae) Qiang Li, Ya Liu, Jian Zhou, Quan Gong, Hua Li, Jiansheng Lai, and Lianman Li
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/25/15 For personal use only.
The Fishery Institute of The Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization, Chengdu, People’s Republic of China Abstract
Keywords
The Gobiobotia filifer is a small economic fish which distributes in the upstream of Yangtze River and its distributaries. For the environmental pollution and overfishing, its population declined drastically in recent decades, so it is essential to protect its resource. In this study, the complete mitochondrial genome sequence of G. filifer was determined with PCR technology, which contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a non-coding control region with the total length of 16,613 bp. The order and composition of genes were similar to most of the other teleost fish. Most of the genes were encoded on heavy strand, except for ND6 genes and eight tRNAs. Just like most other vertebrates, the bias of G and C has been found in different genes/regions. The complete mitochondrial genome sequence of G. filifer would contribute to better understand evolution of this lineage, population genetics, and will help administrative department to make rules and laws to protect this lineage.
Complete mitochondrial genome, cypriniformes, gobiobotia filifer
The Gobiobotia filifer is a small economic fish of Cypriniformes which distributes in the upstream of Yangtze River and its distributaries. We have presented the complete mitochondrial genome of G. filifer, with the GenBank accession number KP325413. The DNA sequence was annotated and compared with the complete mitochondrial genome of Gobiobotia naktongensis (Hwang et al., 2013; Genbank accession number: NC_020464) and Gobiobotia intermedia (Wu, unpublished, Genbank accession number: NC_022931) with Sequin (http:// www.ncbi.nlm.nih.gov/Sequin/download/seq_download.html) and BioEdit 7.1 (Hall, 1998). The contiguous, overlapping segments of the complete mitochondrial genomes of Gobiobotia filifer were amplified and obtained by 22 primers according to the PCR condition of reference (Zhou et al., 2014). The sequences were checked manually and compared with Gobiobotia naktongensis and Gobiobotia intermedia to identify the protein-coding genes, tRNA genes, rRNA genes and a displacement loop (control region) implemented with BioEdit 7.1 (Hall, 1998). The complete mitochondrial genome of G. filifer was 16,613 bp in size with 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a displacement loop (control region, Table 1). Most of the G. filifer mitochondrial genes were encoded on Heavy-Strand (H-strand) except for eight tRNA genes (tRNAGln, Ala, Asn, Cys, Tyr, Ser, Glu and Pro) and ND6 which were encoded on Light-Strand (L-strand). The arrangement and gene numbers were similar to the typical vertebrate mitochondrial
Correspondence: Lianman Li, The Fishery Institute of The Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization, Chengdu 611730, People’s Republic of China. Tel: +86 28 87955508. Fax: +86 27 87955508. E-mail: [email protected]
History Received 5 January 2015 Revised 11 January 2015 Accepted 24 January 2015 Published online 25 March 2015
Table 1. The mtDNA organization of the of G. filifer. Gene/ element Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer tRNAAsp COII tRNALys ATP8 ATP6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu
Position
Space(+) Overlap( )
Length (bp)
1–69 70–1031 1032–1103 1104–2792 2793–2872 2873–3844 3849–3920 3912–3989 3991–4060 4060–5106 5107–5178 5181–5249 5251–5323 5355–5422 5424–5494 5495–7046 7047–7117 7121–7192 7205–7895 7897–7972 7973–8137 8131–8814 8814–9597 9599–9670 9670–10,018 10,020–10,088 10,088–10,384 10,378–11,760 11,761–11,829 11,831–11,897 11,900–11,972 11,972–13,807 13,805–14,325 14,326–14,395
0 0 0 0 0 0 +4 9 +1 1 0 +2 +1 +32 +1 0 0 +3 +12 0 0 7 1 0 1 0 0 7 0 +1 +2 1 4 0
69 962 72 1689 79 972 72 70 70 1047 72 69 73 68 71 1551 71 72 691 76 165 684 784 72 349 69 297 1383 69 67 73 1836 521 70
Start codon
Stop codon
ATG
TAA
ATG
TAA
GTG
TAA
ATG
T
ATG ATG ATG
TAA TAA T
ATG
T
ATG ATG
TAA TAG
ATG ATG
TAG TAG
Strand H H H H H H H L H H H L L L L H L H H H H H H H H H H H H H H H L L
(continued )
2
Q. Li et al.
Mitochondrial DNA, Early Online: 1–2
supported by the grants from Special Fund for Agro-scientific Research in the Public Interest (201203081).
Table 1. Continued. Gene/ element
Position
Space(+) Overlap( )
Length (bp)
Start codon
Stop codon
CYTB tRNAThr tRNAPro D-loop
14,399–15,539 15,540–15,612 15,612–15,681 15,680–16,613
+3 0 1 0
1141 73 70 934
ATG
T
Strand H H L
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/25/15 For personal use only.
ATP 6 and 8, ATPase subunits 6 and 8; bp, base pair(s);COI–III, cytochrome c oxidase subunits I–III; cyt b, cytochrome b; ND1–6, 4L, NADH dehydrogenase subunits 1–6, 4L; tRNA, transfer RNA; 12SrRNA and 16S rRNA, 12S and 16S ribosomal RNA; mtDNA, mitochondrial DNA.
genomes (Peng et al., 2006; Waldbieser et al., 2003; Zhou et al., 2014). ATG was the common start codon for most protein-coding genes except for COI which started with GTG. TAA was the typical stop codon in six protein-coding genes (ND1, ND2, COI, APT8, APT6, ND4L) while TAG was the stop codon of three protein-coding genes (ND4, ND5 and ND6). And the other four genes (COII, COIII, ND3, CYTB) have the incomplete stop codons T which are presumably completed by polyadenylation of the RNA messenger after cleavage (Nardi et al., 2001). There were overlapping nucleotides in certain adjacent tRNA genes and protein-coding genes. There were nine regions of gene overlap (ranging from 1 to 9 bp) and eleven intergenic spacer regions (ranging from 1 to 32 bp, Table 1). Against G bias was found in almost all genes, elements and different statistics regions. The A + T was higher than G+C in above statistics results, which were found in other fishes (Wang et al., 2011; Kartavtsev et al., 2007). The G. filifer is a small economic fish with small population, which limited distribute in the upstream of Yangtze river and its distributaries. But to date, the study about G. filifer even on genus Gobiobotia only involved in taxonomy and phylogeny (Chen, 2001; He, 1991; Hwang et al., 2013; Wu, Unpublished; Zhang & Liu, 1995; Zheng & Yang, 1986), description of the morphological characters of the larvae and fingerlings (Gao, 1998), population genetics (Wang et al., 2014; Zeng et al., 2014). The complete mitochondrial DNA of G. filifer will contribute to study its population genetics, evolutional history, and will help administrative department to make rules and laws to protect this endangered lineage.
Declaration of interest The authors declare no conflict of interest. The authors alone are responsible for the content and writing of the paper. This work was
References Chen M. (2001). Study on the fishes of Cyprinidae from Guangxi Part III. Gobiobotinae, Acheilognathinae and Barbinae. J Liuzhou Vocational Technical College 1:45–52. Gao ZF. (1998). Description of the morphological characters of the larvae and fingerlings of Gobiotia Ichaangensis Fang. Acta Hydrobiologica sinica 12:186–8. Hall TA. (1998). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–8. He SP. (1991). On the anatomy and phylogeny of the Gobiobotine fishes. Acta Zootaxonomica Sinica 16:490–5. Hwang DS, Byeon HK, Lee JS. (2013). Complete mitochondrial genome of the freshwater gudgeon, Gobiobotia nakdongensis (Cypriniformes, Gobioninae). Mitochondrial DNA 24:409–10. Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS. (2007). Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus Siluriformes, Amblycipididae: Genome description and phylogenetic considerations inferred from the Cytb and 16S rRNA genes. Gene 396:13–27. Nardi FC, Carapelli A, Fanciulli PP, Dallai R, Frati F. (2001). The complete mitochondrial DNA sequence of the basal hexapod Tetrodontophora bielanensis: Evidence for heteroplasmy and tRNA translocations. Mol Biol Evol 18:1293–304. Peng ZG, Wang J, He SP. (2006). The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376: 290–7. Waldbieser GC, Bilodeau AL, Nonneman DJ. (2003). Complete sequence and characterization of the channel catfish mitochondrial genome. DNA Seq 14:265–77. Wang JJ, Li P, Zhang YG, Peng ZG. (2011). The complete mitochondrial genome of Chinese rare minnow, Gobiocypris rarus (Teleostei: Cypriniformes). Mitochondrial DNA 22:178–80. Wang S, Luo HW, Tian HW, Liu SP, Duan XB. (2014). Status of the population resources of Xenophysogobio boulengeri in the upper reach of Yangtze river. Freshwater Fish 44:35–40. Wu CY. Complete mitochondrial genome of Gobiobotia intermedia (Cypriniformes, Cyprinidae). Unpublished. Zeng XY, Yang ZY, Tian HW, Wang DQ. (2015). Analysis of microsatellite composition in Xenophysogobio nudicorpa using Mi-Seq high throughput sequencing. Freshwater Fish 45:3–7. Zhang E, Liu HZ. (1995). A new species of the genus Gobiobotia from Jiangxi province, China (Cypriniformes: Cyprinidae). Acta Zootaxonomica Sinica 20:249–52. Zheng ML, Yang JP. (1986). A new species of the genus Gobiobotia (Pisces, Cyprinidae). Acta Zool Sinica 32:58–61. Zhou CJ, Li BH, Ma LY, Zhao YJ, Kong XH. (2014). The complete mitogenome of natural triploid Carassius auratus in Qihe river. Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2014.908367.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Gobiobotia filifer (Teleostei, Cypriniformes: Cyprinidae) Qiang Li, Ya Liu, Jian Zhou, Quan Gong, Hua Li, Jiansheng Lai, and Lianman Li
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/25/15 For personal use only.
The Fishery Institute of The Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization, Chengdu, People’s Republic of China Abstract
Keywords
The Gobiobotia filifer is a small economic fish which distributes in the upstream of Yangtze River and its distributaries. For the environmental pollution and overfishing, its population declined drastically in recent decades, so it is essential to protect its resource. In this study, the complete mitochondrial genome sequence of G. filifer was determined with PCR technology, which contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a non-coding control region with the total length of 16,613 bp. The order and composition of genes were similar to most of the other teleost fish. Most of the genes were encoded on heavy strand, except for ND6 genes and eight tRNAs. Just like most other vertebrates, the bias of G and C has been found in different genes/regions. The complete mitochondrial genome sequence of G. filifer would contribute to better understand evolution of this lineage, population genetics, and will help administrative department to make rules and laws to protect this lineage.
Complete mitochondrial genome, cypriniformes, gobiobotia filifer
The Gobiobotia filifer is a small economic fish of Cypriniformes which distributes in the upstream of Yangtze River and its distributaries. We have presented the complete mitochondrial genome of G. filifer, with the GenBank accession number KP325413. The DNA sequence was annotated and compared with the complete mitochondrial genome of Gobiobotia naktongensis (Hwang et al., 2013; Genbank accession number: NC_020464) and Gobiobotia intermedia (Wu, unpublished, Genbank accession number: NC_022931) with Sequin (http:// www.ncbi.nlm.nih.gov/Sequin/download/seq_download.html) and BioEdit 7.1 (Hall, 1998). The contiguous, overlapping segments of the complete mitochondrial genomes of Gobiobotia filifer were amplified and obtained by 22 primers according to the PCR condition of reference (Zhou et al., 2014). The sequences were checked manually and compared with Gobiobotia naktongensis and Gobiobotia intermedia to identify the protein-coding genes, tRNA genes, rRNA genes and a displacement loop (control region) implemented with BioEdit 7.1 (Hall, 1998). The complete mitochondrial genome of G. filifer was 16,613 bp in size with 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a displacement loop (control region, Table 1). Most of the G. filifer mitochondrial genes were encoded on Heavy-Strand (H-strand) except for eight tRNA genes (tRNAGln, Ala, Asn, Cys, Tyr, Ser, Glu and Pro) and ND6 which were encoded on Light-Strand (L-strand). The arrangement and gene numbers were similar to the typical vertebrate mitochondrial
Correspondence: Lianman Li, The Fishery Institute of The Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization, Chengdu 611730, People’s Republic of China. Tel: +86 28 87955508. Fax: +86 27 87955508. E-mail: [email protected]
History Received 5 January 2015 Revised 11 January 2015 Accepted 24 January 2015 Published online 25 March 2015
Table 1. The mtDNA organization of the of G. filifer. Gene/ element Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer tRNAAsp COII tRNALys ATP8 ATP6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu
Position
Space(+) Overlap( )
Length (bp)
1–69 70–1031 1032–1103 1104–2792 2793–2872 2873–3844 3849–3920 3912–3989 3991–4060 4060–5106 5107–5178 5181–5249 5251–5323 5355–5422 5424–5494 5495–7046 7047–7117 7121–7192 7205–7895 7897–7972 7973–8137 8131–8814 8814–9597 9599–9670 9670–10,018 10,020–10,088 10,088–10,384 10,378–11,760 11,761–11,829 11,831–11,897 11,900–11,972 11,972–13,807 13,805–14,325 14,326–14,395
0 0 0 0 0 0 +4 9 +1 1 0 +2 +1 +32 +1 0 0 +3 +12 0 0 7 1 0 1 0 0 7 0 +1 +2 1 4 0
69 962 72 1689 79 972 72 70 70 1047 72 69 73 68 71 1551 71 72 691 76 165 684 784 72 349 69 297 1383 69 67 73 1836 521 70
Start codon
Stop codon
ATG
TAA
ATG
TAA
GTG
TAA
ATG
T
ATG ATG ATG
TAA TAA T
ATG
T
ATG ATG
TAA TAG
ATG ATG
TAG TAG
Strand H H H H H H H L H H H L L L L H L H H H H H H H H H H H H H H H L L
(continued )
2
Q. Li et al.
Mitochondrial DNA, Early Online: 1–2
supported by the grants from Special Fund for Agro-scientific Research in the Public Interest (201203081).
Table 1. Continued. Gene/ element
Position
Space(+) Overlap( )
Length (bp)
Start codon
Stop codon
CYTB tRNAThr tRNAPro D-loop
14,399–15,539 15,540–15,612 15,612–15,681 15,680–16,613
+3 0 1 0
1141 73 70 934
ATG
T
Strand H H L
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/25/15 For personal use only.
ATP 6 and 8, ATPase subunits 6 and 8; bp, base pair(s);COI–III, cytochrome c oxidase subunits I–III; cyt b, cytochrome b; ND1–6, 4L, NADH dehydrogenase subunits 1–6, 4L; tRNA, transfer RNA; 12SrRNA and 16S rRNA, 12S and 16S ribosomal RNA; mtDNA, mitochondrial DNA.
genomes (Peng et al., 2006; Waldbieser et al., 2003; Zhou et al., 2014). ATG was the common start codon for most protein-coding genes except for COI which started with GTG. TAA was the typical stop codon in six protein-coding genes (ND1, ND2, COI, APT8, APT6, ND4L) while TAG was the stop codon of three protein-coding genes (ND4, ND5 and ND6). And the other four genes (COII, COIII, ND3, CYTB) have the incomplete stop codons T which are presumably completed by polyadenylation of the RNA messenger after cleavage (Nardi et al., 2001). There were overlapping nucleotides in certain adjacent tRNA genes and protein-coding genes. There were nine regions of gene overlap (ranging from 1 to 9 bp) and eleven intergenic spacer regions (ranging from 1 to 32 bp, Table 1). Against G bias was found in almost all genes, elements and different statistics regions. The A + T was higher than G+C in above statistics results, which were found in other fishes (Wang et al., 2011; Kartavtsev et al., 2007). The G. filifer is a small economic fish with small population, which limited distribute in the upstream of Yangtze river and its distributaries. But to date, the study about G. filifer even on genus Gobiobotia only involved in taxonomy and phylogeny (Chen, 2001; He, 1991; Hwang et al., 2013; Wu, Unpublished; Zhang & Liu, 1995; Zheng & Yang, 1986), description of the morphological characters of the larvae and fingerlings (Gao, 1998), population genetics (Wang et al., 2014; Zeng et al., 2014). The complete mitochondrial DNA of G. filifer will contribute to study its population genetics, evolutional history, and will help administrative department to make rules and laws to protect this endangered lineage.
Declaration of interest The authors declare no conflict of interest. The authors alone are responsible for the content and writing of the paper. This work was
References Chen M. (2001). Study on the fishes of Cyprinidae from Guangxi Part III. Gobiobotinae, Acheilognathinae and Barbinae. J Liuzhou Vocational Technical College 1:45–52. Gao ZF. (1998). Description of the morphological characters of the larvae and fingerlings of Gobiotia Ichaangensis Fang. Acta Hydrobiologica sinica 12:186–8. Hall TA. (1998). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–8. He SP. (1991). On the anatomy and phylogeny of the Gobiobotine fishes. Acta Zootaxonomica Sinica 16:490–5. Hwang DS, Byeon HK, Lee JS. (2013). Complete mitochondrial genome of the freshwater gudgeon, Gobiobotia nakdongensis (Cypriniformes, Gobioninae). Mitochondrial DNA 24:409–10. Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS. (2007). Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus Siluriformes, Amblycipididae: Genome description and phylogenetic considerations inferred from the Cytb and 16S rRNA genes. Gene 396:13–27. Nardi FC, Carapelli A, Fanciulli PP, Dallai R, Frati F. (2001). The complete mitochondrial DNA sequence of the basal hexapod Tetrodontophora bielanensis: Evidence for heteroplasmy and tRNA translocations. Mol Biol Evol 18:1293–304. Peng ZG, Wang J, He SP. (2006). The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376: 290–7. Waldbieser GC, Bilodeau AL, Nonneman DJ. (2003). Complete sequence and characterization of the channel catfish mitochondrial genome. DNA Seq 14:265–77. Wang JJ, Li P, Zhang YG, Peng ZG. (2011). The complete mitochondrial genome of Chinese rare minnow, Gobiocypris rarus (Teleostei: Cypriniformes). Mitochondrial DNA 22:178–80. Wang S, Luo HW, Tian HW, Liu SP, Duan XB. (2014). Status of the population resources of Xenophysogobio boulengeri in the upper reach of Yangtze river. Freshwater Fish 44:35–40. Wu CY. Complete mitochondrial genome of Gobiobotia intermedia (Cypriniformes, Cyprinidae). Unpublished. Zeng XY, Yang ZY, Tian HW, Wang DQ. (2015). Analysis of microsatellite composition in Xenophysogobio nudicorpa using Mi-Seq high throughput sequencing. Freshwater Fish 45:3–7. Zhang E, Liu HZ. (1995). A new species of the genus Gobiobotia from Jiangxi province, China (Cypriniformes: Cyprinidae). Acta Zootaxonomica Sinica 20:249–52. Zheng ML, Yang JP. (1986). A new species of the genus Gobiobotia (Pisces, Cyprinidae). Acta Zool Sinica 32:58–61. Zhou CJ, Li BH, Ma LY, Zhao YJ, Kong XH. (2014). The complete mitogenome of natural triploid Carassius auratus in Qihe river. Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2014.908367.
