http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.913161
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Paracanthobrama guichenoti Fukuan Du, Gangchun Xu, Zhijuan Nie, Pao Xu, and Ruobo Gu
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/10/15 For personal use only.
Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China Abstract
Keywords
In this study, we sequenced the complete mitochondrial genome of Paracanthobrama guichenoti. This mitochondrial genome, consisting of 16,607 base pairs, encoded 13 proteincoding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding control region as those found in other vertebrates, with the gene synteny identical to that of typical vertebrates. Control region (D-Loop), of 932 bp in length, is located between tRNAPhe and tRNALeu. The overall base composition of the heavy strand shows T 28.4%, C 24.6%, A 31.2% and G 15.7%, with an AT bias of 59.6%.
Cyprinidae, mitochondrial genome, Paracanthobrama guichenoti
Paracanthobrama guichenoti (Cypriniformes: Cyprinidae) is a commercially important aquaculture species due to its nutritive value and delicacy (Gu et al., 2008). They are widely distributed in Hong River basin in Yunnan, China and expected from the Viet Namese part of the basin. Paracanthobrama guichenoti is a medium-sized, demersal, and was an endemic species to China. Previous studies of P. guichenoti gave only the characterization of morphological data, and no molecular data were reported. In this study, the complete mitochondrial genome of P. guichenoti was first determined (KJ645748). The complete mitochondrial genome of Paracanthobrama guichenoti (16,607 bp in length) consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region (CR) (Table 1). The arrangement of all genes was identical to other Cyprinidae (Wang et al., 2014; Xie et al., 2014; Yue et al., 2014, Yu et al., 2014). Most of the genes are encoded on the heavy strand (H-strand), except for the ND6 and eight tRNA genes (tRNA-Gln, -Ala, -Asn, -Cys, -Tyr, -Ser, -Glu, and -Pro) encoded on the L-strand. The overall base composition values for the H-strand are 28.4% for T, 24.6% for C, 31.2% for A, and 15.7% for G, with a A + T bias of 59.6%. Except for COI start with GTG, the remaining 12 protein-coding genes start with ATG. Within stop codons of 13 protein-coding genes, three kinds of codon were found in P. guichenoti: TAA (ND2, COI, ATPase 6, ND 4L, ND5, ND6); TAG (ND1, ATPase 8); and incomplete stop codon T (COa, COb, ND3, ND4, Cytb). This feature is common among vertebrate mitochondrial protein-coding genes, and these incomplete stop codons are presumably completed as TAA via posttranscriptional polyadenylation (Ojala et al., 1981). The two ribosomal RNA genes, 12srR NA (952 bp) and 16SrR NA
Correspondence: Ruobo Gu, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China. Tel: +86 051085390029. Fax: +86-0510-85390026. E-mail: [email protected]
History Received 2 April 2014 Accepted 5 April 2014 Published online 29 April 2014
(1685 bp), are located between tRNAPhe and tRNALeu and are separated by tRNAVal gene. As in other vertebrates (Chang et al., 2014; Li et al., 2014; Zhou et al., 2014), P. guichenoti has two non-coding regions within its mitogenome: a CR (932 bp) located between tRNAPro and tRNAPhe. Table 1. Characteristics of the mitochondrial genome of P. guichenoti.
Gene/Elemen From tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer tRNAAsp COII tRNALys ATPase8 ATPase6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer
1 70 1029 1101 2789 2866 3845 3915 3987 4056 5102 5176 5246 5351 5419 5491 7042 7115 7199 7890 7967 8124 8808 9592 9664 10,013 10,083 10,373 11,755 11,824
To 69 1028 1100 2788 2864 3840 3916 3985 4055 5098 5173 5244 5318 5418 5489 7041 7112 7186 7889 7965 8131 8808 9591 9663 10,012 10,082 10,379 11,753 11,823 11,892
Length Intergenic (bp) Start Stop nucleotides* Strand# 69 959 72 1688 76 975 72 71 69 1043 72 69 73 68 71 1551 71 72 691 76 165 684 784 72 349 70 297 1381 69 69
ATG TAG
ATG TAA
GTG TAA ATG
T
ATG TAG ATG TAA ATG T ATG
T
ATG TAA ATG T
0 0 0 0 1 4 2 1 0 3 2 1 32 0 1 0 2 12 0 1 7 1 0 0 0 0 7 1 0 1
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 (continued )
2
F. Du et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Gene/Elemen From tRNALeu ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro D-Loop
11,894 11,967 13,799 14,321 14,394 15,535 15,606 15,676
To
Length Intergenic (bp) Start Stop nucleotides* Strand#
11,966 73 13,802 1836 ATG TAA 14,320 522 ATG TAA 14,389 69 15,534 1141 ATG T 15,606 72 15,675 70 16,607 932
0 4 0 4 0 1 0 0
H H L L H H L H
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/10/15 For personal use only.
*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 strand, respectively.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was supported by a grant from the National Key Technology R&D Program of China (2012BAD26B05) and Three New Projects of Agricultural Aquaculture Program of Jiangsu Province (PJ2010-55).
References Chang CH, Jabado RW, Lin YS, Shao KT. (2014). The complete mitochondrial genome of the sand tiger shark,
Carcharias taurus (Chondrichthyes, Odontaspididae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2013.845761. Li Q, Xu R, Shu H, Chen Q, Huang J. (2014). The complete mitochondrial genome of the Zig-zag eel Mastacembelus armatus (Teleostei, Mastacembelidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2014.892102. Gu RB, Xu GC, Dan H, Wen HB, Wang YF, Zhang SL. (2008). Evaluation of fish quality and analysis of the nutritive compositions of Paracanthobrama guichenoti Bleeker. J Ocean Univ China 32: 263–8. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Wang FY, Jean CT, Chen YJ, Lin KY, Liu MY. (2014). The complete mitochondrial genome sequence of Belligobio nummifer (Cypriniformes, Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2014.898293. Xie P, Ao M, Liu C, Zhang Z, Zhang Y, Niu J, Karjan A, Ma X. (2014). The complete mitochondrial genome of Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2014.880893. Yu Y, Yi W, Ma Z, Yang R, Shen J. (2014). The complete mitochondrial genome of Rhodeus fangi (Cypriniformes, Cyprinidae, Acheilognathinae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2014.892079. Yue X, Zhou C, Shi J, Zou Y. (2014). The complete mitochondrial genome sequence of Schizothorax dolichonema (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. DOI: doi:10.3109/19401736.2014.895999. Zhou C, Wang X, Guan L, He S. (2014). The complete mitochondrial genome of Clarias fuscus (Teleostei, Siluriformes: Clariidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2013.823177.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Paracanthobrama guichenoti Fukuan Du, Gangchun Xu, Zhijuan Nie, Pao Xu, and Ruobo Gu
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/10/15 For personal use only.
Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China Abstract
Keywords
In this study, we sequenced the complete mitochondrial genome of Paracanthobrama guichenoti. This mitochondrial genome, consisting of 16,607 base pairs, encoded 13 proteincoding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding control region as those found in other vertebrates, with the gene synteny identical to that of typical vertebrates. Control region (D-Loop), of 932 bp in length, is located between tRNAPhe and tRNALeu. The overall base composition of the heavy strand shows T 28.4%, C 24.6%, A 31.2% and G 15.7%, with an AT bias of 59.6%.
Cyprinidae, mitochondrial genome, Paracanthobrama guichenoti
Paracanthobrama guichenoti (Cypriniformes: Cyprinidae) is a commercially important aquaculture species due to its nutritive value and delicacy (Gu et al., 2008). They are widely distributed in Hong River basin in Yunnan, China and expected from the Viet Namese part of the basin. Paracanthobrama guichenoti is a medium-sized, demersal, and was an endemic species to China. Previous studies of P. guichenoti gave only the characterization of morphological data, and no molecular data were reported. In this study, the complete mitochondrial genome of P. guichenoti was first determined (KJ645748). The complete mitochondrial genome of Paracanthobrama guichenoti (16,607 bp in length) consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region (CR) (Table 1). The arrangement of all genes was identical to other Cyprinidae (Wang et al., 2014; Xie et al., 2014; Yue et al., 2014, Yu et al., 2014). Most of the genes are encoded on the heavy strand (H-strand), except for the ND6 and eight tRNA genes (tRNA-Gln, -Ala, -Asn, -Cys, -Tyr, -Ser, -Glu, and -Pro) encoded on the L-strand. The overall base composition values for the H-strand are 28.4% for T, 24.6% for C, 31.2% for A, and 15.7% for G, with a A + T bias of 59.6%. Except for COI start with GTG, the remaining 12 protein-coding genes start with ATG. Within stop codons of 13 protein-coding genes, three kinds of codon were found in P. guichenoti: TAA (ND2, COI, ATPase 6, ND 4L, ND5, ND6); TAG (ND1, ATPase 8); and incomplete stop codon T (COa, COb, ND3, ND4, Cytb). This feature is common among vertebrate mitochondrial protein-coding genes, and these incomplete stop codons are presumably completed as TAA via posttranscriptional polyadenylation (Ojala et al., 1981). The two ribosomal RNA genes, 12srR NA (952 bp) and 16SrR NA
Correspondence: Ruobo Gu, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China. Tel: +86 051085390029. Fax: +86-0510-85390026. E-mail: [email protected]
History Received 2 April 2014 Accepted 5 April 2014 Published online 29 April 2014
(1685 bp), are located between tRNAPhe and tRNALeu and are separated by tRNAVal gene. As in other vertebrates (Chang et al., 2014; Li et al., 2014; Zhou et al., 2014), P. guichenoti has two non-coding regions within its mitogenome: a CR (932 bp) located between tRNAPro and tRNAPhe. Table 1. Characteristics of the mitochondrial genome of P. guichenoti.
Gene/Elemen From tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer tRNAAsp COII tRNALys ATPase8 ATPase6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer
1 70 1029 1101 2789 2866 3845 3915 3987 4056 5102 5176 5246 5351 5419 5491 7042 7115 7199 7890 7967 8124 8808 9592 9664 10,013 10,083 10,373 11,755 11,824
To 69 1028 1100 2788 2864 3840 3916 3985 4055 5098 5173 5244 5318 5418 5489 7041 7112 7186 7889 7965 8131 8808 9591 9663 10,012 10,082 10,379 11,753 11,823 11,892
Length Intergenic (bp) Start Stop nucleotides* Strand# 69 959 72 1688 76 975 72 71 69 1043 72 69 73 68 71 1551 71 72 691 76 165 684 784 72 349 70 297 1381 69 69
ATG TAG
ATG TAA
GTG TAA ATG
T
ATG TAG ATG TAA ATG T ATG
T
ATG TAA ATG T
0 0 0 0 1 4 2 1 0 3 2 1 32 0 1 0 2 12 0 1 7 1 0 0 0 0 7 1 0 1
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 (continued )
2
F. Du et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Gene/Elemen From tRNALeu ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro D-Loop
11,894 11,967 13,799 14,321 14,394 15,535 15,606 15,676
To
Length Intergenic (bp) Start Stop nucleotides* Strand#
11,966 73 13,802 1836 ATG TAA 14,320 522 ATG TAA 14,389 69 15,534 1141 ATG T 15,606 72 15,675 70 16,607 932
0 4 0 4 0 1 0 0
H H L L H H L H
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/10/15 For personal use only.
*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 strand, respectively.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was supported by a grant from the National Key Technology R&D Program of China (2012BAD26B05) and Three New Projects of Agricultural Aquaculture Program of Jiangsu Province (PJ2010-55).
References Chang CH, Jabado RW, Lin YS, Shao KT. (2014). The complete mitochondrial genome of the sand tiger shark,
Carcharias taurus (Chondrichthyes, Odontaspididae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2013.845761. Li Q, Xu R, Shu H, Chen Q, Huang J. (2014). The complete mitochondrial genome of the Zig-zag eel Mastacembelus armatus (Teleostei, Mastacembelidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2014.892102. Gu RB, Xu GC, Dan H, Wen HB, Wang YF, Zhang SL. (2008). Evaluation of fish quality and analysis of the nutritive compositions of Paracanthobrama guichenoti Bleeker. J Ocean Univ China 32: 263–8. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Wang FY, Jean CT, Chen YJ, Lin KY, Liu MY. (2014). The complete mitochondrial genome sequence of Belligobio nummifer (Cypriniformes, Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2014.898293. Xie P, Ao M, Liu C, Zhang Z, Zhang Y, Niu J, Karjan A, Ma X. (2014). The complete mitochondrial genome of Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2014.880893. Yu Y, Yi W, Ma Z, Yang R, Shen J. (2014). The complete mitochondrial genome of Rhodeus fangi (Cypriniformes, Cyprinidae, Acheilognathinae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2014.892079. Yue X, Zhou C, Shi J, Zou Y. (2014). The complete mitochondrial genome sequence of Schizothorax dolichonema (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. DOI: doi:10.3109/19401736.2014.895999. Zhou C, Wang X, Guan L, He S. (2014). The complete mitochondrial genome of Clarias fuscus (Teleostei, Siluriformes: Clariidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2013.823177.
