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 Hoeven’s mullet-goby Hemigobius hoevenii (Bleeker) (Teleostei, Gobiidae) Shih-Pin Huang, Chia-Ning Shen & I-Shiung Chen To cite this article: Shih-Pin Huang, Chia-Ning Shen & I-Shiung Chen (2014): The complete mitochondrial genome of Hoeven’s mullet-goby Hemigobius hoevenii (Bleeker) (Teleostei, Gobiidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.913156
Published online: 29 Apr 2014.
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Date: 27 October 2015, At: 01:12
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.913156
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Hoeven’s mullet-goby Hemigobius hoevenii (Bleeker) (Teleostei, Gobiidae) Shih-Pin Huang1, Chia-Ning Shen2, and I-Shiung Chen1 Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan, ROC and 2Genomic Research Center, Academia Sinica, Taipei, Taiwan, ROC
Downloaded by [Gazi University] at 01:12 27 October 2015
1
Abstract
Keywords
In this study, the complete mitochondrial genome of Hoeven’s mullet-goby Hemigobius hoevenii (Bleeker, 1851) collected from Malay Peninsula has been amplified and sequenced. The complete mitochondrial genome is 16,469 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region (CR) and 1 light-strand replication origin (OL). The overall base composition of H. hoevenii is 27.1% for A, 26.6% for T, 29.0% for C, 17.3% for G, with higher AT content 53.7%. This study will contribute for understanding the phylogenetic approach of Hemigobius species as well as the related genera of gobiid fishes.
Complete mitogenome Hemigobius hoevenii, Gobiidae, Hoeven’s mullet-goby
The Hoeven’s mullet-goby Hemigobius hoevenii (Bleeker, 1851) is the type species of Hemigobius and distributes in brackish habitats and lagoons of East and Southeast Asia (Huang et al., 2013). The fish was collected from Matang mangrove, Malay Peninsula and preserved in 95% ethanol. Total DNA was extracted using the High Pure DNA Extraction Kit (Roche Applied Sciences, Penzberg, Germany). The complete mitochondrial genome was amplified and sequenced in its entirety using a long PCR technique (Miya & Nishida, 1999) with 18 pairs of primers, which were designed based on the alignment of different gobioid fishes (Chiang et al., 2013; Huang et al., 2014a,b; Kim et al., 2004a,b; Quan et al., 2012). The complete mitochondrial genome of Hemigobius hoevenii was similar to most other vertebrates (Chen, 2013; Kim et al., 2004a,b; Miya & Nishida, 1999; Quan et al., 2012; Shi et al.,
History Received 1 April 2014 Accepted 5 April 2014 Published online 29 April 2014
2012), it has a typical vertebrate mitochondrial gene arrangement, and with a size of 16,469 bp (GenBank KF916564) in length including 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, 1 control region and 1 lightstrand replication origin (OL) (Table 1). Except for ND6 and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UGA), tRNAGlu and tRNAPro) encoded on the L-strand, other genes were encoded on the H-strand. The overall base composition of H. hoevenii is 27.1% for A, 26.6% for T, 29.0% for C, 17.3% for G, the higher AT content (53.7%) is similar to other gobioid fishes (Chiang et al., 2013; Huang et al., 2014a,b; Jin et al., 2013; Kim et al., 2004a,b; Sun et al., 2013). All 13 protein-coding genes shared the same start codon ATG, except for COI (start codon GTG). It is also important to note that two of 13 protein-coding genes were inferred to termination with
Table 1. Organization of mitochondrial genome in H. hoevenii. Gene/element tRNA-Phe 12SrRNA tRNA-Val 16SrRNA tRNA-Leu1(UAA) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala
From 1 69 1013 1085 2760 2834 3811 3880 3950 4019 5066 5139
To 68 1012 1084 2759 2833 3808 3880 3950 4018 5065 5136 5206
Length (bp) 68 944 72 1675 74 975 70 71 69 1047 71 68
Start codon
Stop codon
Anticondon GAA TAC TAA
ATG
TAA GAT TTG CAT
ATG
TAA TCA TGC
Intergenic nucleotides* 0 0 0 0 0 2 1 1 0 0 2 1
Strand H H H H H H H L H H H L (continued )
Correspondence: I-S. Chen, Institute of Marine Biology, National Taiwan Ocean University, Keelung 202, Taiwan, ROC. Tel: +88 624622192 ext. 5305. Fax: +88 6224633152. E-mail: [email protected]
2
S.-P. Huang et al.
Mitochondrial DNA, Early Online: 1–2
Downloaded by [Gazi University] at 01:12 27 October 2015
Table 1. Continued
Gene/element
From
To
Length (bp)
tRNA-Asn OL tRNA-Cys tRNA-Tyr COI tRNA-Ser1(UGA) tRNA-Asp COII tRNA-Lys ATPase8 ATPase6 COIII tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser2(GCU) tRNA-Leu2(UAG) ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro D-Loop(CR)
5208 5281 5315 5379 5451 7005 7079 7154 7845 7921 8079 8762 9546 9617 9966 10,035 10,325 11,709 11,773 11,845 11,918 13,753 14,275 14,349 15,490 15,565 15,635
5280 5314 5378 5449 7004 7075 7150 7844 7919 8085 8762 9546 9616 9967 10,034 10,331 11,710 11,772 11,844 11,917 13,756 14,274 14,343 15,489 15,561 15,634 16,469
73 34 64 71 1554 71 72 691 75 165 684 785 71 351 69 297 1386 64 72 73 1839 522 69 1141 72 70 835
Start codon
Stop codon
Anticondon GTT GCA GTA
GTG
TAA TGA GTC
ATG
T– –
ATG ATG ATG
TAG TAA TA–
ATG
TAG
ATG ATG
TAA AGG
TTT
TCC TCG GTG GCT TAG ATG ATG
TAA TAA
ATG
T– –
TTC TGT TGG
Intergenic nucleotides* 0 0 0 1 0 3 3 0 1 7 1 1 0 2 0 7 2 0 0 0 4 0 5 0 3 0 0
Strand 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 –
*Intergenic nucleotides: negative number indicates that adjacent genes overlap.
an incomplete stop codon T– – (COII and Cytb); one of them was inferred to termination with an stop codon TA– (COIII); seven of them shared the typical termination codon TAA (ND1, ND2, COI, ATPase 6, ND4L, ND5 and ND6); two of them shared TAG (ATPase 8 and ND3) as the typical termination codon; one terminated with AGG (ND4). Many gobioid fish species also used such incomplete codon structure as signal to halt the process of protein translation (Jin et al., 2012, 2013; Kim et al., 2004a,b; Quan et al., 2012; Shi et al., 2012; Sun et al., 2013). The longest one was ND5 gene (1839 bp) in all protein coding genes, whereas the shortest is ATPase 8 gene (165 bp). The Dloop was 835 bp in length which was similar to other gobioid fishes, and is located between tRNAPro and tRNAPhe genes. The 12Sr RNA and 16Sr RNA genes were 944 and 1675 bp in length respectively, the two genes located between tRNAPhe and tRNALeu genes, and they were separated by tRNAVal. The present result will contribute for further understanding the molecular phylogeny of Hemigobius species as well as related genera of gobiid fishes.
Declaration of interest The authors declare no competing materials in the preparation and execution of this manuscript. The authors are responsible for the content and writing of this paper. The corresponding author (I-S. C.) wishes to thank the CEO, NTOU for the grant support for aquatic biodiversity research team. The current work was also supported by the grants from the National Science Council, Taipei for the corresponding author.
References Bleeker P. (1851). Vijfde bijdrage tot de kennis der ichthyologische fauna van Borneo met beschrijving van eenige nieuwe soorten van zoetwatervisschen. Natuurkundig Tijdschrift voor Nederlandsch-Indie 2:415–42. Chen IS. (2013). The complete mitochondrial genome of Chinese sucker Myxocyprinus asiaticus (Cypriniformes, Catostomidae). Mitochondrial DNA 24:680–2.
Chiang TY, Chen IS, Lin HD, Chang WB, Ju YM. (2013). Complete mitochondrial genome of Sicyopterus japonicus (Perciformes, Gobiidae). Mitochondrial DNA 24:191–3. Huang SP, Chen IS, Shao KT. (2013). The molecular phylogeny of genus Hemigobius (Teleostei: Gobiidae), with the confirmation of validity of Hemigobius crassa (Herre, 1945). J Mar Sci Tech 21:86–93. Huang SP, Shen CN, Chen IS. (2014a). The complete mitochondrial genome of the Abe’s mangrove goby Mugilogobius abei (Teleostei, Gobiidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2013.819494. Huang SP, Shen CN, Chen IS. (2014b). The complete mitochondrial genome of the Java fat-nose goby Pseudogobius javanicus (Teleostei, Gobiidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2013.819502. Jin XX, Wang RX, Zhao SL, Xu TJ, Shi G. (2012). Complete mitochondrial genome of the striped sandgoby Acentrogobius pflaumii (Perciformes, gobiidae). Mitochondrial DNA 23:420–2. Jin XX, Zhao SL, Sun YN. (2013). Complete mitochondrial genome sequence and structure of control region of the Amoya chusanensis (Perciformes, Gobioidei). Mitochondrial DNA 24:403–5. Kim YJ, Kweon HS, Kim IC, Lee YM, Kim JM, Lee JS. (2004a). The complete mitochondrial genome of the floating goby, Gymnogobius petschiliensis (Perciformes, Gobiidae). Mol Cells 17:446–53. Kim IC, Kweon HS, Kim YJ, Kim CB, Gye MC, Lee WO, Lee YS, Lee JS. (2004b). The complete mitochondrial genome of the javeline goby Acanthogobius hasta (Perciformes, Gobiidae) and phylogenetic considerations. Gene 336:147–53. Miya M, Nishida M. (1999). Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): First example of transfer RNA gene arrangement in bony fish. Mar Biotechnol 1:416–26. Quan X, Jin X, Wang R, Xu T, Shi G. (2012). Complete mitochondrial genome of the walking goby Scartelaos histophorus (Perceformes, Gobiidae). Mitochondrial DNA 23:298–300. Shi G, Jin X, Zhao S, Xu T, Wang R. (2012). Complete mitochondrial genome of Trypauchen vagina (Perciformes, Gobioidei). Mitochondrial DNA 23:151–3. Sun YN, Jin XX, Zhao SL, Liu XZ. (2013). Mitochondrial genome of Cryptocentrus yatsui (Perciformes, Gobioidei) and phylogenetic consideration within the genus Cryptocentrus. Mitochondrial DNA 24: 376–8.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Hoeven’s mullet-goby Hemigobius hoevenii (Bleeker) (Teleostei, Gobiidae) Shih-Pin Huang, Chia-Ning Shen & I-Shiung Chen To cite this article: Shih-Pin Huang, Chia-Ning Shen & I-Shiung Chen (2014): The complete mitochondrial genome of Hoeven’s mullet-goby Hemigobius hoevenii (Bleeker) (Teleostei, Gobiidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.913156
Published online: 29 Apr 2014.
Submit your article to this journal
Article views: 10
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: [Gazi University]
Date: 27 October 2015, At: 01:12
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.913156
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Hoeven’s mullet-goby Hemigobius hoevenii (Bleeker) (Teleostei, Gobiidae) Shih-Pin Huang1, Chia-Ning Shen2, and I-Shiung Chen1 Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan, ROC and 2Genomic Research Center, Academia Sinica, Taipei, Taiwan, ROC
Downloaded by [Gazi University] at 01:12 27 October 2015
1
Abstract
Keywords
In this study, the complete mitochondrial genome of Hoeven’s mullet-goby Hemigobius hoevenii (Bleeker, 1851) collected from Malay Peninsula has been amplified and sequenced. The complete mitochondrial genome is 16,469 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region (CR) and 1 light-strand replication origin (OL). The overall base composition of H. hoevenii is 27.1% for A, 26.6% for T, 29.0% for C, 17.3% for G, with higher AT content 53.7%. This study will contribute for understanding the phylogenetic approach of Hemigobius species as well as the related genera of gobiid fishes.
Complete mitogenome Hemigobius hoevenii, Gobiidae, Hoeven’s mullet-goby
The Hoeven’s mullet-goby Hemigobius hoevenii (Bleeker, 1851) is the type species of Hemigobius and distributes in brackish habitats and lagoons of East and Southeast Asia (Huang et al., 2013). The fish was collected from Matang mangrove, Malay Peninsula and preserved in 95% ethanol. Total DNA was extracted using the High Pure DNA Extraction Kit (Roche Applied Sciences, Penzberg, Germany). The complete mitochondrial genome was amplified and sequenced in its entirety using a long PCR technique (Miya & Nishida, 1999) with 18 pairs of primers, which were designed based on the alignment of different gobioid fishes (Chiang et al., 2013; Huang et al., 2014a,b; Kim et al., 2004a,b; Quan et al., 2012). The complete mitochondrial genome of Hemigobius hoevenii was similar to most other vertebrates (Chen, 2013; Kim et al., 2004a,b; Miya & Nishida, 1999; Quan et al., 2012; Shi et al.,
History Received 1 April 2014 Accepted 5 April 2014 Published online 29 April 2014
2012), it has a typical vertebrate mitochondrial gene arrangement, and with a size of 16,469 bp (GenBank KF916564) in length including 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, 1 control region and 1 lightstrand replication origin (OL) (Table 1). Except for ND6 and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UGA), tRNAGlu and tRNAPro) encoded on the L-strand, other genes were encoded on the H-strand. The overall base composition of H. hoevenii is 27.1% for A, 26.6% for T, 29.0% for C, 17.3% for G, the higher AT content (53.7%) is similar to other gobioid fishes (Chiang et al., 2013; Huang et al., 2014a,b; Jin et al., 2013; Kim et al., 2004a,b; Sun et al., 2013). All 13 protein-coding genes shared the same start codon ATG, except for COI (start codon GTG). It is also important to note that two of 13 protein-coding genes were inferred to termination with
Table 1. Organization of mitochondrial genome in H. hoevenii. Gene/element tRNA-Phe 12SrRNA tRNA-Val 16SrRNA tRNA-Leu1(UAA) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala
From 1 69 1013 1085 2760 2834 3811 3880 3950 4019 5066 5139
To 68 1012 1084 2759 2833 3808 3880 3950 4018 5065 5136 5206
Length (bp) 68 944 72 1675 74 975 70 71 69 1047 71 68
Start codon
Stop codon
Anticondon GAA TAC TAA
ATG
TAA GAT TTG CAT
ATG
TAA TCA TGC
Intergenic nucleotides* 0 0 0 0 0 2 1 1 0 0 2 1
Strand H H H H H H H L H H H L (continued )
Correspondence: I-S. Chen, Institute of Marine Biology, National Taiwan Ocean University, Keelung 202, Taiwan, ROC. Tel: +88 624622192 ext. 5305. Fax: +88 6224633152. E-mail: [email protected]
2
S.-P. Huang et al.
Mitochondrial DNA, Early Online: 1–2
Downloaded by [Gazi University] at 01:12 27 October 2015
Table 1. Continued
Gene/element
From
To
Length (bp)
tRNA-Asn OL tRNA-Cys tRNA-Tyr COI tRNA-Ser1(UGA) tRNA-Asp COII tRNA-Lys ATPase8 ATPase6 COIII tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser2(GCU) tRNA-Leu2(UAG) ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro D-Loop(CR)
5208 5281 5315 5379 5451 7005 7079 7154 7845 7921 8079 8762 9546 9617 9966 10,035 10,325 11,709 11,773 11,845 11,918 13,753 14,275 14,349 15,490 15,565 15,635
5280 5314 5378 5449 7004 7075 7150 7844 7919 8085 8762 9546 9616 9967 10,034 10,331 11,710 11,772 11,844 11,917 13,756 14,274 14,343 15,489 15,561 15,634 16,469
73 34 64 71 1554 71 72 691 75 165 684 785 71 351 69 297 1386 64 72 73 1839 522 69 1141 72 70 835
Start codon
Stop codon
Anticondon GTT GCA GTA
GTG
TAA TGA GTC
ATG
T– –
ATG ATG ATG
TAG TAA TA–
ATG
TAG
ATG ATG
TAA AGG
TTT
TCC TCG GTG GCT TAG ATG ATG
TAA TAA
ATG
T– –
TTC TGT TGG
Intergenic nucleotides* 0 0 0 1 0 3 3 0 1 7 1 1 0 2 0 7 2 0 0 0 4 0 5 0 3 0 0
Strand 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 –
*Intergenic nucleotides: negative number indicates that adjacent genes overlap.
an incomplete stop codon T– – (COII and Cytb); one of them was inferred to termination with an stop codon TA– (COIII); seven of them shared the typical termination codon TAA (ND1, ND2, COI, ATPase 6, ND4L, ND5 and ND6); two of them shared TAG (ATPase 8 and ND3) as the typical termination codon; one terminated with AGG (ND4). Many gobioid fish species also used such incomplete codon structure as signal to halt the process of protein translation (Jin et al., 2012, 2013; Kim et al., 2004a,b; Quan et al., 2012; Shi et al., 2012; Sun et al., 2013). The longest one was ND5 gene (1839 bp) in all protein coding genes, whereas the shortest is ATPase 8 gene (165 bp). The Dloop was 835 bp in length which was similar to other gobioid fishes, and is located between tRNAPro and tRNAPhe genes. The 12Sr RNA and 16Sr RNA genes were 944 and 1675 bp in length respectively, the two genes located between tRNAPhe and tRNALeu genes, and they were separated by tRNAVal. The present result will contribute for further understanding the molecular phylogeny of Hemigobius species as well as related genera of gobiid fishes.
Declaration of interest The authors declare no competing materials in the preparation and execution of this manuscript. The authors are responsible for the content and writing of this paper. The corresponding author (I-S. C.) wishes to thank the CEO, NTOU for the grant support for aquatic biodiversity research team. The current work was also supported by the grants from the National Science Council, Taipei for the corresponding author.
References Bleeker P. (1851). Vijfde bijdrage tot de kennis der ichthyologische fauna van Borneo met beschrijving van eenige nieuwe soorten van zoetwatervisschen. Natuurkundig Tijdschrift voor Nederlandsch-Indie 2:415–42. Chen IS. (2013). The complete mitochondrial genome of Chinese sucker Myxocyprinus asiaticus (Cypriniformes, Catostomidae). Mitochondrial DNA 24:680–2.
Chiang TY, Chen IS, Lin HD, Chang WB, Ju YM. (2013). Complete mitochondrial genome of Sicyopterus japonicus (Perciformes, Gobiidae). Mitochondrial DNA 24:191–3. Huang SP, Chen IS, Shao KT. (2013). The molecular phylogeny of genus Hemigobius (Teleostei: Gobiidae), with the confirmation of validity of Hemigobius crassa (Herre, 1945). J Mar Sci Tech 21:86–93. Huang SP, Shen CN, Chen IS. (2014a). The complete mitochondrial genome of the Abe’s mangrove goby Mugilogobius abei (Teleostei, Gobiidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2013.819494. Huang SP, Shen CN, Chen IS. (2014b). The complete mitochondrial genome of the Java fat-nose goby Pseudogobius javanicus (Teleostei, Gobiidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2013.819502. Jin XX, Wang RX, Zhao SL, Xu TJ, Shi G. (2012). Complete mitochondrial genome of the striped sandgoby Acentrogobius pflaumii (Perciformes, gobiidae). Mitochondrial DNA 23:420–2. Jin XX, Zhao SL, Sun YN. (2013). Complete mitochondrial genome sequence and structure of control region of the Amoya chusanensis (Perciformes, Gobioidei). Mitochondrial DNA 24:403–5. Kim YJ, Kweon HS, Kim IC, Lee YM, Kim JM, Lee JS. (2004a). The complete mitochondrial genome of the floating goby, Gymnogobius petschiliensis (Perciformes, Gobiidae). Mol Cells 17:446–53. Kim IC, Kweon HS, Kim YJ, Kim CB, Gye MC, Lee WO, Lee YS, Lee JS. (2004b). The complete mitochondrial genome of the javeline goby Acanthogobius hasta (Perciformes, Gobiidae) and phylogenetic considerations. Gene 336:147–53. Miya M, Nishida M. (1999). Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): First example of transfer RNA gene arrangement in bony fish. Mar Biotechnol 1:416–26. Quan X, Jin X, Wang R, Xu T, Shi G. (2012). Complete mitochondrial genome of the walking goby Scartelaos histophorus (Perceformes, Gobiidae). Mitochondrial DNA 23:298–300. Shi G, Jin X, Zhao S, Xu T, Wang R. (2012). Complete mitochondrial genome of Trypauchen vagina (Perciformes, Gobioidei). Mitochondrial DNA 23:151–3. Sun YN, Jin XX, Zhao SL, Liu XZ. (2013). Mitochondrial genome of Cryptocentrus yatsui (Perciformes, Gobioidei) and phylogenetic consideration within the genus Cryptocentrus. Mitochondrial DNA 24: 376–8.
