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
Complete mitochondrial genome of catfish Eutropiichthys vacha (Hamilton, 1822) Lashari Punhal, Muhammad Younis Laghari, Baradi Waryani, Shaista Jalbani, Naeem Tariq Narejo & Yan Zhang To cite this article: Lashari Punhal, Muhammad Younis Laghari, Baradi Waryani, Shaista Jalbani, Naeem Tariq Narejo & Yan Zhang (2015): Complete mitochondrial genome of catfish Eutropiichthys vacha (Hamilton, 1822), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1007357
Published online: 29 Jan 2015.
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Date: 07 November 2015, At: 14:44
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1007357
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of catfish Eutropiichthys vacha (Hamilton, 1822) Lashari Punhal1, Muhammad Younis Laghari1, Baradi Waryani1, Shaista Jalbani1, Naeem Tariq Narejo1, and Yan Zhang2 Department of Fresh Water Biology and Fisheries, University of Sindh, Jamshoro, Pakistan and 2Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
Downloaded by [Imperial College London Library] at 14:44 07 November 2015
1
Abstract
Keywords
Complete mitochondrial genome of catfish, Eutropiichthys vacha, was isolated by LA PCR (TakaRa LAtaq, Dalian, China); and sequenced by Sanger’s method to obtain the complete mitochondrial genome, which is listed Critically Endangered and Red-listed species. The complete mitogenome was 16,478 bp in length and contains 13 typical vertebrate proteincoding genes, 2 rRNA and 22 tRNA genes. The whole genome base composition was estimated to be 31.06% A, 27.59% C, 15.65% G, and 25.68% T. The complete mitochondrial genome of catfish, E. vacha provides the fundamental tool for genetic breeding and conservation studies.
Endangered, Eutropiichthys vacha, mitochondrial genome
The freshwater catfish Eutropiichthys vacha, an excellent food fish, is an economically important inland water teleost fish, which is quite palatable as a table fish found in lakes of Bangladesh, Pakistan, India, Burma and Thailand (Talwar & Jhingran, 1991). The smaller size has often been placed in aquaria while large sizes are used as food. Largely, demands exceed the supply, particularly in India and neighboring countries such as Pakistan, SriLanka and Bangladesh (Afsar, 1990). Eutropiichthys vacha is widely distributed from the larger freshwater rivers of the Gangetic provinces in India, Nepal, Bhutan and Bangladesh (Ferraris & Vari, 2007). Keeping in mind the paucity of information on the biology, the present study focuses on the complete mitochondrial genome of the species. In this current study, we determined the complete mitochondrial genome of catfish E. vacha. Total DNA
History Received 6 January 2015 Accepted 10 January 2015 Published online 29 January 2015
was extracted using QIAGEN DNeasy Blood & Tissue kit (Qiagen, Valencia, CA). The complete mitogenome generated was 16,588 bp in length. The complete mitogenome of E. vacha has been deposited in GenBank with an accession number (AB919123). Mitogenome was amplified in two large overlapping fragments by long PCR (TakaRa LAtaq, Dalian, China), using the specific primers designed by previously reported two genes of same species. The complete E. vacha mitogenome sequence (GenBank No. AB919123) is 16,478 bp in length. The overall characteristics, including its overall organization and the gene arrangement pattern, are identical to that of the typical vertebrate mitogenome. The complete mitogenome contains 13 proteincoding genes, 2 rRNA, 22 tRNA genes and 1 putative control region (Table 1). The average base composition of the E. vacha
Table 1. Organization and profile of the catfish, Eutropiichthys vacha mitochondrial genome. Gene
Start phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UAA) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla
1 67 1026 1098 2767 2842 3822 3893 3963 4033 5078 5151
Stop 66 1025 1097 2766 2841 3816 3893 3963 4032 5077 5148 5219
Size (bp) 66 958 71 1668 74 974 71 70 69 1044 70 68
Start
Stop
Anticodon
Nucleotide*
Strandy
GAA
– –
TAC
0 0 0 0 +6 0 0 0 0 +3
H H H H H H H L H H H L
TAA ATG
TAA GAT TTG CAT
ATG
T CCA TGC
(continued )
Correspondence: Lashari Punhal, Department of Fresh Water Biology and Fisheries, University of Sindh, Jamshoro 76080, Pakistan. E-mail: [email protected] Yan Zhang, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China. E-mail: [email protected]
2
L. Punhal et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Gene
Downloaded by [Imperial College London Library] at 14:44 07 November 2015
Asn
tRNA OL tRNACys tRNATyr COX1 tRNASer(UGA) tRNAAsp COX2 tRNALys ATPase 8 ATPase 6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(UGC) tRNALeu(UAG) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro D-loop
Start
Stop
Size (bp)
5221 5294 5326 5396 5468 7019 7094 7191 7858 7933 8091 8774 9558 9631 9980 10,051 10,341 11,722 11,792 11,861 11,933 13,761 14,302 14,372 15,510 15,580 15,651
5293 5326 5392 5466 7018 7089 7166 7857 7931 8100 8773 9557 9630 9979 10,050 10,347 11,721 11,791 11,858 11,932 13,759 14,279 14,370 15,509 15,581 15,650 16,478
73 32 67 70 1551 70 71 690 73 167 682 783 72 348 70 296 1380 69 66 71 1826 518 69 1137 72 70 827
Start
Stop
Anticodon
Nucleotide*
Strandy
GTT
+2 – 0 +2 +2 0 +5 +25 0 +2 9 0 0 0 0 0 6 0 1 +3 0 +2 +23 +2 0 1 0
L – L L H L H H H H H H H H H H H H H H H L L H H H –
GCA GTA GTG
TAA TGA GTC
ATG
T
ATG ATG ATG
TAA TAA T
ATG
T
ATG ATG
TAA T
ATG ATG
TAA TAG
ATG
T
TCC TCG
GTG TAG TTC TGT TGG
*Numbers correspond to the nucleotides separating different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. yH and L denote heavy and light strands, respectively.
complete mitogenome is 31.06% A, 27.59% C, 15.65% G, and 25.68% T. All protein-coding genes except (NADH6) were encoded on heavy strand (H strand). Fourteen tRNA were encoded on heavy strand and remainder were encoded on light strand (L strand). The E. vacha mtDNA genome conforms to the consensus gene order of other fish (mtDNA) genome (Table 1). Twelve protein-coding genes use ATG as start codon (NADH1, NADH2, COX2, ATPase 8, ATPase 6, COX3, NADH3, NADH4L, NADH4, NADH5, NADH6 and CYTB), one gene use GTG (COX1). Six open-reading frames use incomplete stop codon T** (NADH2, COX2, COX3, NAHD3, NADH4, and CYTB); Seven genes use stop codon as TAA (NAHD1, COX1, ATPase 8, ATPase 6, NADH4L and NADH5). One gene (COX2) uses TAG as stop codon, respectively. The control region D-loop is located between tRNApro and tRNAphe with 827 bp in length.
Declaration of interest This work was supported by the introduction of advanced agricultural science and technology key projects (2011-G12) and Special Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fishery Sciences (2012C013). The authors report no conflict of interest. The authors alone are responsible for the content and writing of the article.
References Afsar MR. (1990). Food and feeding habits of a teleostean fish (Ham.) in the Ganga river system. J Freshwater Biol 2:159–67. Ferraris CJ, Vari RP. (2007). Revision of the Catfishes of the genus Eutropiichthys, with the description of two new species (Siluriformes: Schilbidae). Copeia 4:866–85. Talwar PK, Jhingran AG. (1991). Inland fishes of India and adjacent countries, Vol. 2. Front cover. Rotterdam: A.A. Balkema.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of catfish Eutropiichthys vacha (Hamilton, 1822) Lashari Punhal, Muhammad Younis Laghari, Baradi Waryani, Shaista Jalbani, Naeem Tariq Narejo & Yan Zhang To cite this article: Lashari Punhal, Muhammad Younis Laghari, Baradi Waryani, Shaista Jalbani, Naeem Tariq Narejo & Yan Zhang (2015): Complete mitochondrial genome of catfish Eutropiichthys vacha (Hamilton, 1822), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1007357
Published online: 29 Jan 2015.
Submit your article to this journal
Article views: 8
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Imperial College London Library]
Date: 07 November 2015, At: 14:44
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1007357
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of catfish Eutropiichthys vacha (Hamilton, 1822) Lashari Punhal1, Muhammad Younis Laghari1, Baradi Waryani1, Shaista Jalbani1, Naeem Tariq Narejo1, and Yan Zhang2 Department of Fresh Water Biology and Fisheries, University of Sindh, Jamshoro, Pakistan and 2Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
Downloaded by [Imperial College London Library] at 14:44 07 November 2015
1
Abstract
Keywords
Complete mitochondrial genome of catfish, Eutropiichthys vacha, was isolated by LA PCR (TakaRa LAtaq, Dalian, China); and sequenced by Sanger’s method to obtain the complete mitochondrial genome, which is listed Critically Endangered and Red-listed species. The complete mitogenome was 16,478 bp in length and contains 13 typical vertebrate proteincoding genes, 2 rRNA and 22 tRNA genes. The whole genome base composition was estimated to be 31.06% A, 27.59% C, 15.65% G, and 25.68% T. The complete mitochondrial genome of catfish, E. vacha provides the fundamental tool for genetic breeding and conservation studies.
Endangered, Eutropiichthys vacha, mitochondrial genome
The freshwater catfish Eutropiichthys vacha, an excellent food fish, is an economically important inland water teleost fish, which is quite palatable as a table fish found in lakes of Bangladesh, Pakistan, India, Burma and Thailand (Talwar & Jhingran, 1991). The smaller size has often been placed in aquaria while large sizes are used as food. Largely, demands exceed the supply, particularly in India and neighboring countries such as Pakistan, SriLanka and Bangladesh (Afsar, 1990). Eutropiichthys vacha is widely distributed from the larger freshwater rivers of the Gangetic provinces in India, Nepal, Bhutan and Bangladesh (Ferraris & Vari, 2007). Keeping in mind the paucity of information on the biology, the present study focuses on the complete mitochondrial genome of the species. In this current study, we determined the complete mitochondrial genome of catfish E. vacha. Total DNA
History Received 6 January 2015 Accepted 10 January 2015 Published online 29 January 2015
was extracted using QIAGEN DNeasy Blood & Tissue kit (Qiagen, Valencia, CA). The complete mitogenome generated was 16,588 bp in length. The complete mitogenome of E. vacha has been deposited in GenBank with an accession number (AB919123). Mitogenome was amplified in two large overlapping fragments by long PCR (TakaRa LAtaq, Dalian, China), using the specific primers designed by previously reported two genes of same species. The complete E. vacha mitogenome sequence (GenBank No. AB919123) is 16,478 bp in length. The overall characteristics, including its overall organization and the gene arrangement pattern, are identical to that of the typical vertebrate mitogenome. The complete mitogenome contains 13 proteincoding genes, 2 rRNA, 22 tRNA genes and 1 putative control region (Table 1). The average base composition of the E. vacha
Table 1. Organization and profile of the catfish, Eutropiichthys vacha mitochondrial genome. Gene
Start phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UAA) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla
1 67 1026 1098 2767 2842 3822 3893 3963 4033 5078 5151
Stop 66 1025 1097 2766 2841 3816 3893 3963 4032 5077 5148 5219
Size (bp) 66 958 71 1668 74 974 71 70 69 1044 70 68
Start
Stop
Anticodon
Nucleotide*
Strandy
GAA
– –
TAC
0 0 0 0 +6 0 0 0 0 +3
H H H H H H H L H H H L
TAA ATG
TAA GAT TTG CAT
ATG
T CCA TGC
(continued )
Correspondence: Lashari Punhal, Department of Fresh Water Biology and Fisheries, University of Sindh, Jamshoro 76080, Pakistan. E-mail: [email protected] Yan Zhang, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China. E-mail: [email protected]
2
L. Punhal et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Gene
Downloaded by [Imperial College London Library] at 14:44 07 November 2015
Asn
tRNA OL tRNACys tRNATyr COX1 tRNASer(UGA) tRNAAsp COX2 tRNALys ATPase 8 ATPase 6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(UGC) tRNALeu(UAG) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro D-loop
Start
Stop
Size (bp)
5221 5294 5326 5396 5468 7019 7094 7191 7858 7933 8091 8774 9558 9631 9980 10,051 10,341 11,722 11,792 11,861 11,933 13,761 14,302 14,372 15,510 15,580 15,651
5293 5326 5392 5466 7018 7089 7166 7857 7931 8100 8773 9557 9630 9979 10,050 10,347 11,721 11,791 11,858 11,932 13,759 14,279 14,370 15,509 15,581 15,650 16,478
73 32 67 70 1551 70 71 690 73 167 682 783 72 348 70 296 1380 69 66 71 1826 518 69 1137 72 70 827
Start
Stop
Anticodon
Nucleotide*
Strandy
GTT
+2 – 0 +2 +2 0 +5 +25 0 +2 9 0 0 0 0 0 6 0 1 +3 0 +2 +23 +2 0 1 0
L – L L H L H H H H H H H H H H H H H H H L L H H H –
GCA GTA GTG
TAA TGA GTC
ATG
T
ATG ATG ATG
TAA TAA T
ATG
T
ATG ATG
TAA T
ATG ATG
TAA TAG
ATG
T
TCC TCG
GTG TAG TTC TGT TGG
*Numbers correspond to the nucleotides separating different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. yH and L denote heavy and light strands, respectively.
complete mitogenome is 31.06% A, 27.59% C, 15.65% G, and 25.68% T. All protein-coding genes except (NADH6) were encoded on heavy strand (H strand). Fourteen tRNA were encoded on heavy strand and remainder were encoded on light strand (L strand). The E. vacha mtDNA genome conforms to the consensus gene order of other fish (mtDNA) genome (Table 1). Twelve protein-coding genes use ATG as start codon (NADH1, NADH2, COX2, ATPase 8, ATPase 6, COX3, NADH3, NADH4L, NADH4, NADH5, NADH6 and CYTB), one gene use GTG (COX1). Six open-reading frames use incomplete stop codon T** (NADH2, COX2, COX3, NAHD3, NADH4, and CYTB); Seven genes use stop codon as TAA (NAHD1, COX1, ATPase 8, ATPase 6, NADH4L and NADH5). One gene (COX2) uses TAG as stop codon, respectively. The control region D-loop is located between tRNApro and tRNAphe with 827 bp in length.
Declaration of interest This work was supported by the introduction of advanced agricultural science and technology key projects (2011-G12) and Special Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fishery Sciences (2012C013). The authors report no conflict of interest. The authors alone are responsible for the content and writing of the article.
References Afsar MR. (1990). Food and feeding habits of a teleostean fish (Ham.) in the Ganga river system. J Freshwater Biol 2:159–67. Ferraris CJ, Vari RP. (2007). Revision of the Catfishes of the genus Eutropiichthys, with the description of two new species (Siluriformes: Schilbidae). Copeia 4:866–85. Talwar PK, Jhingran AG. (1991). Inland fishes of India and adjacent countries, Vol. 2. Front cover. Rotterdam: A.A. Balkema.
