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
Mitochondrial genome of the Marbled goby (Oxyeleotris marmorata) Zhen-Yu Yang, Hong-Wei Liang, Zhong Li, Dan Wang & Gui-Wei Zou To cite this article: Zhen-Yu Yang, Hong-Wei Liang, Zhong Li, Dan Wang & Gui-Wei Zou (2014): Mitochondrial genome of the Marbled goby (Oxyeleotris marmorata), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.928873
Published online: 25 Jun 2014.
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Date: 17 November 2015, At: 01:06
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.928873
MITOGENOME ANNOUNCEMENT
Mitochondrial genome of the Marbled goby (Oxyeleotris marmorata) Zhen-Yu Yang1,2, Hong-Wei Liang2, Zhong Li2, Dan Wang2, and Gui-Wei Zou2 College of Fisheries, Huazhong Agricultural University, Wuhan, P.R. China and 2Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan, P.R. China
Downloaded by [University of Otago] at 01:06 17 November 2015
1
Abstract
Keywords
The marble goby is a carnivorous fish native to freshwater in Asia-Pacific region, and it is marketed as a high-valued fish in some Asia countries such as China, Thailand and Vietnam. This study presents the complete mitochondrial genome of O. marmorata, which is 16,525 bp length with the genome organization and gene order being identical to that of the typical vertebrate.
Genome, marbled goby, mitochondrial
Marbled Goby (Oxyeleotris marmorata), a carnivorous fish native to freshwater in Asia-Pacific region, belonging to the Family Eleotridae (Sleepers) and Subfamily Butinae, and can be found in Asia, including the Mekong and Chao Phraya basins, Malay Peninsula, Indochina, Philippine and Indonesia. It can survive on land for several days with an air-breather, and its natural habitat includes canals, rivers, reservoirs and swamps (Roberts, 1993). It is also a high-valued species in many Asian countries, and feeding on small fishes, shrimps, aquatic insects, mollusks and crabs (Larson & Murdy, 2001). It is perhaps the largest goby, capable of growing to 41 kg, and is considered a delicacy over much of eastern Asia. Since O. marmorata has a high commercial value, it has been cultured in Malaysia, Cambodia, Vietnam and Indonesia (Jee, 1980; Luong et al., 2005; Hoa & Yi, 2007). It was introduced to China in 1986, and now it is marketed as a high-valued fish in China. This study reports the complete mitochondrial genome sequence of O. marmorata, which can provide a useful tool for studies on its phylogenetic analysis. One Marbled Goby was collected from the aquaculture farm in Guangzhou city. Total genomic DNA was isolated from tail fin with the TIANamp Genomic DNA Kit (Tiangen Biotech, Beijing, China). Protein-coding genes were identified by similarity of predicted amino-acid sequence with known mitochondrial protein sequences. The total length of the Marbled Goby mitochondrial genome (GenBank accession number KF711995) was 16,525 bp, and the overall nucleotide composition was A 28.7%, T 24.9%, G 15.5%, C 30.9% and with an AT content of 53.6%. The complete mtDNA contained 13 protein-coding genes, 22 tRNA genes, 2rRNA genes, and a displacement loop (D-loop) locus (Table 1). Except for the ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. All these 13 protein-coding genes start with the ATG start codon except COX1 gene, which starts with the GTG start codon and is typical in all bony fishes (Wang et al., 2013). Seven protein-coding genes Correspondence: Gui-Wei Zou, Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan 4300700, P.R. China. Tel: +86-27-81780088. Fax: +86-27-81780088. E-mail: [email protected].
History Received 24 May 2014 Accepted 25 May 2014 Published online 25 June 2014
Table 1. Characteristics of the mitochondrial genome of O. marmorata. Site Locus Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COX1 tRNASer(UCN) tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGN) tRNALeu(CUN) ND5 ND6 tRNAGlu CYTB tRNAThr tRNAPro D-loop
From
To
1 69 1023 1097 2780 2856 3834 3903 3973 4042 5088 5163 5233 5343 5409 5481 7035 7109 7187 7878 7955 8113 8796 9581 9653 10,002 10,071 10,361 11,742 11,811 11,884 11,957 13,792 14,314 14,388 15,529 15,600 15,670
68 1022 1094 2779 2855 3830 3903 3973 4041 5087 5159 5231 5305 5408 5479 7034 7105 7175 7877 7953 8122 8796 9579 9652 10,001 10,070 10,367 11,741 11,810 11,879 11,956 13,795 14,313 14,382 15,528 15,600 15,669 16,525
Codon Length Intergenic bp Start Stop Strand+ Nucleotides* 68 954 72 1683 76 975 70 71 69 1046 72 69 73 66 71 1554 71 67 691 76 168 684 784 72 349 69 297 1381 69 69 73 1839 522 69 1141 72 70 856
ATG TAG
ATG TA–
GTG TAA ATG T– – ATG TAA ATG TAA ATG T– – ATG T– – ATG TAA ATG T– –
ATG TAA ATG TAG ATG T– –
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 H H L
0 0 2 0 0 3 1 1 0 0 3 1 37 0 1 0 3 11 0 1 10 1 1 0 0 0 7 0 0 4 0 4 0 5 0 1 0
*Numbers correspond to the nucleotides separating different genes. Negative numbers indicate overlapping nucleotides between adjacent genes; +H and L indicate genes transcribed on the heavy and light strand, respectively.
Downloaded by [University of Otago] at 01:06 17 November 2015
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Z.-Y. Yang et al.
(ND1, COX1, ND4L, ND5, ND6, ATP6 and ATP8) have the TAA or TAG termination codon, and other genes (ND2, COX2, COX3, ND3, ND4 and CYTB) with the incomplete termination codons. Some overlapping sequences between protein-coding genes are identified: ATP8 overlaps with ATP6 for 10 bp, ATP6 overlaps with COX3 for 1 bp, ND4L overlaps with ND4 for 7 bp, which were located on the same strand; although ND5 overlaps with ND6 for 4 bp as well, they are encoded on opposite strands. The rRNA gene boundaries are estimated via nucleotide sequence alignments with other Gobioidei species. The tRNA genes vary from 66 to 76 bp in length and employ the anticodons typical of vertebrate mt-tRNAs. The 16S rRNA (1683 bp) and 12S rRNA (954 bp) were located between tRNAPhe gene and tRNA-Leu gene, and separated by tRNA-Val gene on the heavy strand. The D-loop of O. marmorata was 856 bp in size and is characterized by conserved sequence blocks (CSBs), which was found in the 30 end of the control region which appear to be involved in positioning RNA polymerase both for transcription and for priming replication (Shadel & Clayton, 1997). The CSBs (1–3) and CSBs (D-F) occured at positions 658– 675, 727–742, 769–787, 376–402, 338–361, 282–303 bp.
Acknowledgements The authors are grateful to Mr. Yang for his assistance in sample collection. They also appreciate the valuable comments of the editor on this work. This research was supported by the Fundamental Research Funds for the Central Universities (2013SC14) of China, Special Basic Work Fund of Science and Technology (2013FY110700), and Special
Mitochondrial DNA, Early Online: 1–2
Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fishery Sciences (2014A11JC05).
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Hoa NP, Yi Y. (2007). Prey ingestin and live food selectivity of marble goby (Oxyeleotris marmorata) using rice field prawn (Macrobrachium lanchesteri) as prey. Aquaculture 273:443–8. Jee AK. (1980). Some problems in the cage culture of marble goby (Oxyeleotris marmorata Bleeker). Aquaculture 20:229. DOI:10.1016/ 0044-8486(80)90112-X. Larson HK, Murdy EO. (2001). Suborder Gobioidei: Eleotridae-sleepers (gudgeons). In: Carpenter KE, Niem VH, editors. FAO Species Identification Guide for Fishery Purposes. The living marine resources of the western central Pacific. Vol. 6. Bony Fishes Part 4 (Labridae to Latimeriidae), Estuarine Crocodiles. Rome: FAO. p. 3574–7. Luong VC, Yi Y, Lin CK. (2005). Cove culture of marble goby (Oxyeleotris marmorata Bleeker) and carps in Tri An Reservoir of Vietnam. Aquaculture 244:97–107. Roberts TR. (1993). Artisanal fisheries and fish ecology below the great waterfalls of the Mekong River in southern Laos. Nat Hist Bull Siam Soc 41:31–62. Shadel GS, Clayton DA. (1997). Mitochondrial DNA maintenance in vertebrates. Annu Rev Biochem 66:409–35. Wang XY, Cao L, Liang HW, Li Z, Zou GW. (2013). Mitochondrial genome of the Shorthead catfish (Pelteobagrus eupogon). Mitochondrial DNA 24:1–2.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Mitochondrial genome of the Marbled goby (Oxyeleotris marmorata) Zhen-Yu Yang, Hong-Wei Liang, Zhong Li, Dan Wang & Gui-Wei Zou To cite this article: Zhen-Yu Yang, Hong-Wei Liang, Zhong Li, Dan Wang & Gui-Wei Zou (2014): Mitochondrial genome of the Marbled goby (Oxyeleotris marmorata), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.928873
Published online: 25 Jun 2014.
Submit your article to this journal
Article views: 12
View related articles
View Crossmark data
Citing articles: 2 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 Otago]
Date: 17 November 2015, At: 01:06
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.928873
MITOGENOME ANNOUNCEMENT
Mitochondrial genome of the Marbled goby (Oxyeleotris marmorata) Zhen-Yu Yang1,2, Hong-Wei Liang2, Zhong Li2, Dan Wang2, and Gui-Wei Zou2 College of Fisheries, Huazhong Agricultural University, Wuhan, P.R. China and 2Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan, P.R. China
Downloaded by [University of Otago] at 01:06 17 November 2015
1
Abstract
Keywords
The marble goby is a carnivorous fish native to freshwater in Asia-Pacific region, and it is marketed as a high-valued fish in some Asia countries such as China, Thailand and Vietnam. This study presents the complete mitochondrial genome of O. marmorata, which is 16,525 bp length with the genome organization and gene order being identical to that of the typical vertebrate.
Genome, marbled goby, mitochondrial
Marbled Goby (Oxyeleotris marmorata), a carnivorous fish native to freshwater in Asia-Pacific region, belonging to the Family Eleotridae (Sleepers) and Subfamily Butinae, and can be found in Asia, including the Mekong and Chao Phraya basins, Malay Peninsula, Indochina, Philippine and Indonesia. It can survive on land for several days with an air-breather, and its natural habitat includes canals, rivers, reservoirs and swamps (Roberts, 1993). It is also a high-valued species in many Asian countries, and feeding on small fishes, shrimps, aquatic insects, mollusks and crabs (Larson & Murdy, 2001). It is perhaps the largest goby, capable of growing to 41 kg, and is considered a delicacy over much of eastern Asia. Since O. marmorata has a high commercial value, it has been cultured in Malaysia, Cambodia, Vietnam and Indonesia (Jee, 1980; Luong et al., 2005; Hoa & Yi, 2007). It was introduced to China in 1986, and now it is marketed as a high-valued fish in China. This study reports the complete mitochondrial genome sequence of O. marmorata, which can provide a useful tool for studies on its phylogenetic analysis. One Marbled Goby was collected from the aquaculture farm in Guangzhou city. Total genomic DNA was isolated from tail fin with the TIANamp Genomic DNA Kit (Tiangen Biotech, Beijing, China). Protein-coding genes were identified by similarity of predicted amino-acid sequence with known mitochondrial protein sequences. The total length of the Marbled Goby mitochondrial genome (GenBank accession number KF711995) was 16,525 bp, and the overall nucleotide composition was A 28.7%, T 24.9%, G 15.5%, C 30.9% and with an AT content of 53.6%. The complete mtDNA contained 13 protein-coding genes, 22 tRNA genes, 2rRNA genes, and a displacement loop (D-loop) locus (Table 1). Except for the ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. All these 13 protein-coding genes start with the ATG start codon except COX1 gene, which starts with the GTG start codon and is typical in all bony fishes (Wang et al., 2013). Seven protein-coding genes Correspondence: Gui-Wei Zou, Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan 4300700, P.R. China. Tel: +86-27-81780088. Fax: +86-27-81780088. E-mail: [email protected].
History Received 24 May 2014 Accepted 25 May 2014 Published online 25 June 2014
Table 1. Characteristics of the mitochondrial genome of O. marmorata. Site Locus Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COX1 tRNASer(UCN) tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGN) tRNALeu(CUN) ND5 ND6 tRNAGlu CYTB tRNAThr tRNAPro D-loop
From
To
1 69 1023 1097 2780 2856 3834 3903 3973 4042 5088 5163 5233 5343 5409 5481 7035 7109 7187 7878 7955 8113 8796 9581 9653 10,002 10,071 10,361 11,742 11,811 11,884 11,957 13,792 14,314 14,388 15,529 15,600 15,670
68 1022 1094 2779 2855 3830 3903 3973 4041 5087 5159 5231 5305 5408 5479 7034 7105 7175 7877 7953 8122 8796 9579 9652 10,001 10,070 10,367 11,741 11,810 11,879 11,956 13,795 14,313 14,382 15,528 15,600 15,669 16,525
Codon Length Intergenic bp Start Stop Strand+ Nucleotides* 68 954 72 1683 76 975 70 71 69 1046 72 69 73 66 71 1554 71 67 691 76 168 684 784 72 349 69 297 1381 69 69 73 1839 522 69 1141 72 70 856
ATG TAG
ATG TA–
GTG TAA ATG T– – ATG TAA ATG TAA ATG T– – ATG T– – ATG TAA ATG T– –
ATG TAA ATG TAG ATG T– –
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 H H L
0 0 2 0 0 3 1 1 0 0 3 1 37 0 1 0 3 11 0 1 10 1 1 0 0 0 7 0 0 4 0 4 0 5 0 1 0
*Numbers correspond to the nucleotides separating different genes. Negative numbers indicate overlapping nucleotides between adjacent genes; +H and L indicate genes transcribed on the heavy and light strand, respectively.
Downloaded by [University of Otago] at 01:06 17 November 2015
2
Z.-Y. Yang et al.
(ND1, COX1, ND4L, ND5, ND6, ATP6 and ATP8) have the TAA or TAG termination codon, and other genes (ND2, COX2, COX3, ND3, ND4 and CYTB) with the incomplete termination codons. Some overlapping sequences between protein-coding genes are identified: ATP8 overlaps with ATP6 for 10 bp, ATP6 overlaps with COX3 for 1 bp, ND4L overlaps with ND4 for 7 bp, which were located on the same strand; although ND5 overlaps with ND6 for 4 bp as well, they are encoded on opposite strands. The rRNA gene boundaries are estimated via nucleotide sequence alignments with other Gobioidei species. The tRNA genes vary from 66 to 76 bp in length and employ the anticodons typical of vertebrate mt-tRNAs. The 16S rRNA (1683 bp) and 12S rRNA (954 bp) were located between tRNAPhe gene and tRNA-Leu gene, and separated by tRNA-Val gene on the heavy strand. The D-loop of O. marmorata was 856 bp in size and is characterized by conserved sequence blocks (CSBs), which was found in the 30 end of the control region which appear to be involved in positioning RNA polymerase both for transcription and for priming replication (Shadel & Clayton, 1997). The CSBs (1–3) and CSBs (D-F) occured at positions 658– 675, 727–742, 769–787, 376–402, 338–361, 282–303 bp.
Acknowledgements The authors are grateful to Mr. Yang for his assistance in sample collection. They also appreciate the valuable comments of the editor on this work. This research was supported by the Fundamental Research Funds for the Central Universities (2013SC14) of China, Special Basic Work Fund of Science and Technology (2013FY110700), and Special
Mitochondrial DNA, Early Online: 1–2
Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fishery Sciences (2014A11JC05).
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Hoa NP, Yi Y. (2007). Prey ingestin and live food selectivity of marble goby (Oxyeleotris marmorata) using rice field prawn (Macrobrachium lanchesteri) as prey. Aquaculture 273:443–8. Jee AK. (1980). Some problems in the cage culture of marble goby (Oxyeleotris marmorata Bleeker). Aquaculture 20:229. DOI:10.1016/ 0044-8486(80)90112-X. Larson HK, Murdy EO. (2001). Suborder Gobioidei: Eleotridae-sleepers (gudgeons). In: Carpenter KE, Niem VH, editors. FAO Species Identification Guide for Fishery Purposes. The living marine resources of the western central Pacific. Vol. 6. Bony Fishes Part 4 (Labridae to Latimeriidae), Estuarine Crocodiles. Rome: FAO. p. 3574–7. Luong VC, Yi Y, Lin CK. (2005). Cove culture of marble goby (Oxyeleotris marmorata Bleeker) and carps in Tri An Reservoir of Vietnam. Aquaculture 244:97–107. Roberts TR. (1993). Artisanal fisheries and fish ecology below the great waterfalls of the Mekong River in southern Laos. Nat Hist Bull Siam Soc 41:31–62. Shadel GS, Clayton DA. (1997). Mitochondrial DNA maintenance in vertebrates. Annu Rev Biochem 66:409–35. Wang XY, Cao L, Liang HW, Li Z, Zou GW. (2013). Mitochondrial genome of the Shorthead catfish (Pelteobagrus eupogon). Mitochondrial DNA 24:1–2.
