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 the Trachypithecus francoisi Qin-Yang Jiang, Xue-Yu Yan, Ling-Jing Wei & Yan-Na Huang To cite this article: Qin-Yang Jiang, Xue-Yu Yan, Ling-Jing Wei & Yan-Na Huang (2014): Complete mitochondrial genome of the Trachypithecus francoisi, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.919461
Published online: 27 May 2014.
Submit your article to this journal
Article views: 12
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: [Chinese University of Hong Kong]
Date: 07 November 2015, At: 00:49
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.919461
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the Trachypithecus francoisi Qin-Yang Jiang, Xue-Yu Yan, Ling-Jing Wei, and Yan-Na Huang
Downloaded by [Chinese University of Hong Kong] at 00:49 07 November 2015
College of Animal Science and Technology, Guangxi University, Nanning, China
Abstract
Keywords
In the present study, the complete mitochondrial genome of Trachypithecus francoisi was determined using PCR reactions. The mitochondrial genome is 16,544 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The structural organization and gene order of T. francoisi were equivalent to that of most other vertebrates. The T. francoisi mtDNA could provide useful data for further studies on phylogenetics and conservation genetics of this species.
Mitochondrial genome, structural organization, Trachypithecus francoisi
The Trachypithecus francoisi is a medium sized primate with black crested hair, and has very distinct white sideburns that grow down from ears to the corners of cheeks. Trachypithecus francoisi is endemic to the limestone forests of the tropical and subtropical zones of south-west China and northern Vietnam, the global population of T. francoisi is less than 2000 individuals (Liu et al., 2013; Wang et al., 2011; Zeng et al., 2013), this number is still decreasing. This species is now listed as endangered on the International Union for Conservation of Nature (IUCN) Red list (Bleisch et al., 2008). In the present paper, a frozen blood sample of adult female T. francoisi was provided by Nanning Zoo in Guangxi Province, China. The blood total DNA was extracted by traditional phenol/ chloroform method. Seventeen pairs of primers were designed to PCR amplify the fragments of mitochondrial DNA (mtDNA) of T. francoisi, with each fragment sequence overlapping the next by over 100 bp. The 17 purified PCR products were sequenced directly by the primer walking method, respectively. Each fragment was sequenced more than three copies to ensure the reliability of the data. Sequenced data were analyzed with DNAstar Lasergene 7.0 software (Madison, WI). Overlapping contigs were compiled using SeqMan to assemble a continuous sequence. The locations of protein-coding genes, ribosome RNA (rRNA), transfer RNA (tRNA) and control region were identified by tRNAscan-SE 1.21 (http://lowelab.ucsc.edu/tRNAscan-SE/) and Blastn (http://blast.ncbi.nlm.nih.gov/BLAST/) comparison with other known primate mitochondrial genome. The mitochondrial genome of T. francoisi was firstly sequenced. It was 16,554 bp in length and has been deposited in GenBank (Accession No. KJ174502). The structural organization and gene order of the complete T. francoisi mtDNA was identical that of other typical vertebrates, with the mitochondrial genome containing the following (Table 1): 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region (D-Loop). In the overall base composition of the T. francoisi mtDNA was A ¼ 32.09%, T ¼ 28.97%, C ¼ 26.16% and G ¼ 12.78%. This A + T rich pattern Correspondence: Yan-Na Huang, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi Province 530004, PR China. Tel/Fax: +86 7713235635. E-mail: [email protected]
History Received 13 April 2014 Accepted 24 April 2014 Published online 27 May 2014
Table 1. The structural organization of the T. francoisi mitochondrial genome. Position Gene/elements
Origin
Stop
Size (bp)
Phe
1 71 1037 1107 2706 2782 3753 3822 3892 3961 5003 5079 5149 5223 5248 5314 5386 6925 6998 7068 7756 7830 7988 8671 9455 9524 9873 9943 10,236 11,626 11,696 11,761 11,833 13,634 14,159 14,231 15,375 15,448 15,517
72 1036 1106 2705 2781 3750 3822 3892 3960 5002 5077 5147 5221 5250 5313 5384 6933 6995 7067 7754 7828 7997 8671 9454 9523 9872 9942 10,242 11,612 11,695 11,761 11,832 13,638 14,158 14,226 15,370 15,446 15,516 16,489
70 966 70 1599 76 969 70 71 69 1042 75 69 73 28 66 71 1548 71 70 687 73 168 684 784 69 351 70 300 1377 70 66 72 1806 525 68 1150 72 69 973
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1 tRNASer(UCN) tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro Control region
Strand (sense) H H H H H H H L H H H L 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 H
Codon Start
Stop
ATG
TAA
ATG
T– –
ATG
AGG
ATG
TAA
ATG ATG ATG
TAA TAA T– –
ATG
T– –
ATG ATG
TAA TAA
ATG ATG
TAA AGG
ATG
T– –
Downloaded by [Chinese University of Hong Kong] at 00:49 07 November 2015
2
Q.-Y. Jiang et al.
reflects a typical sequence feature of the vertebrate mitochondrial genome. ND2 gene started with ATT, the start codon of ND3 was ATA, other 11 protein-coding genes started with ATG. ND2, ND3, ND4, COX3 and Cyt b genes had incomplete stop codons of T, ND1 gene end with TAG, ND6 gene was terminated with AGA, the stop codons of the rest protein-coding genes were TAA. The length of 12SrRNA gene was 948 bp and 16SrRNA gene was 1562 bp, 2 genes were separated by the tRNAVal and positioned between the tRNAPhe and tRNALeu(UUR). The 22 tRNA genes ranged in size from 59 bp to 75 bp, which were typical animal mtDNA genes, could be folded into the analogous cloverleaf secondly structure. The light-strand replication origin (OL) positioned in the WANCY tRNA genes cluster and located between tRNAAsn and tRNACys, it might potentially fold into a stable stem-loop secondary structure with a stem comprised of 10 bp and a loop of 12 nucleotides. The length of control region (D-Loop) was 1093 bp, 57.64% A + T rich and flanked by tRNAPro and tRNAPhe genes.
Declaration of interest This article is original, has been written by the stated authors who are all aware of its content and approve its submission, has not been published
Mitochondrial DNA, Early Online: 1–2
previously, it is not under consideration for publication elsewhere, no conflict of interest exists, and if accepted, the article will not be published elsewhere in the same form, in any language, without the written consent of the publisher. This research was partially funded by National Natural Science Foundation of China (81360135) and the Natural Science Foundation of Guangxi province (2012GXNSFBA053041, 2013GXNSFAA019187).
References Bleisch B, Ha MN, Quyet KL, Yongcheng L. (2008). Trachypithecus francoisi. In: IUCN 2013. IUCN Red List of Threatened Species. Version 2013.2. Available at: http://www.iucnredlist.org (Accessed 12 May 2014). Liu ZJ, Wang BS, Nadler T, Liu GJ, Sun T, Huang CM, Zhou QH, et al. (2013). Relatively recent evolution of pelage coloration in Colobinae: Phylogeny and phylogeography of three closely related langur species. PLoS One 8:e61659. Wang SL, Luo Y, Cui GF. (2011). Sleeping site selection of Francois’s langur (Trachypithecus francoisi) in two habitats in Mayanghe National Nature Reserve, Guizhou, China. Primates 52: 51–60. Zeng YJ, Xu JL, Wang Y, Zhou CF. (2013). Habitat association and conservation implications of Endangered Francois’ Langur (Trachypithecus francoisi). PLoS One 8:e75661.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of the Trachypithecus francoisi Qin-Yang Jiang, Xue-Yu Yan, Ling-Jing Wei & Yan-Na Huang To cite this article: Qin-Yang Jiang, Xue-Yu Yan, Ling-Jing Wei & Yan-Na Huang (2014): Complete mitochondrial genome of the Trachypithecus francoisi, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.919461
Published online: 27 May 2014.
Submit your article to this journal
Article views: 12
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: [Chinese University of Hong Kong]
Date: 07 November 2015, At: 00:49
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.919461
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the Trachypithecus francoisi Qin-Yang Jiang, Xue-Yu Yan, Ling-Jing Wei, and Yan-Na Huang
Downloaded by [Chinese University of Hong Kong] at 00:49 07 November 2015
College of Animal Science and Technology, Guangxi University, Nanning, China
Abstract
Keywords
In the present study, the complete mitochondrial genome of Trachypithecus francoisi was determined using PCR reactions. The mitochondrial genome is 16,544 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The structural organization and gene order of T. francoisi were equivalent to that of most other vertebrates. The T. francoisi mtDNA could provide useful data for further studies on phylogenetics and conservation genetics of this species.
Mitochondrial genome, structural organization, Trachypithecus francoisi
The Trachypithecus francoisi is a medium sized primate with black crested hair, and has very distinct white sideburns that grow down from ears to the corners of cheeks. Trachypithecus francoisi is endemic to the limestone forests of the tropical and subtropical zones of south-west China and northern Vietnam, the global population of T. francoisi is less than 2000 individuals (Liu et al., 2013; Wang et al., 2011; Zeng et al., 2013), this number is still decreasing. This species is now listed as endangered on the International Union for Conservation of Nature (IUCN) Red list (Bleisch et al., 2008). In the present paper, a frozen blood sample of adult female T. francoisi was provided by Nanning Zoo in Guangxi Province, China. The blood total DNA was extracted by traditional phenol/ chloroform method. Seventeen pairs of primers were designed to PCR amplify the fragments of mitochondrial DNA (mtDNA) of T. francoisi, with each fragment sequence overlapping the next by over 100 bp. The 17 purified PCR products were sequenced directly by the primer walking method, respectively. Each fragment was sequenced more than three copies to ensure the reliability of the data. Sequenced data were analyzed with DNAstar Lasergene 7.0 software (Madison, WI). Overlapping contigs were compiled using SeqMan to assemble a continuous sequence. The locations of protein-coding genes, ribosome RNA (rRNA), transfer RNA (tRNA) and control region were identified by tRNAscan-SE 1.21 (http://lowelab.ucsc.edu/tRNAscan-SE/) and Blastn (http://blast.ncbi.nlm.nih.gov/BLAST/) comparison with other known primate mitochondrial genome. The mitochondrial genome of T. francoisi was firstly sequenced. It was 16,554 bp in length and has been deposited in GenBank (Accession No. KJ174502). The structural organization and gene order of the complete T. francoisi mtDNA was identical that of other typical vertebrates, with the mitochondrial genome containing the following (Table 1): 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region (D-Loop). In the overall base composition of the T. francoisi mtDNA was A ¼ 32.09%, T ¼ 28.97%, C ¼ 26.16% and G ¼ 12.78%. This A + T rich pattern Correspondence: Yan-Na Huang, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi Province 530004, PR China. Tel/Fax: +86 7713235635. E-mail: [email protected]
History Received 13 April 2014 Accepted 24 April 2014 Published online 27 May 2014
Table 1. The structural organization of the T. francoisi mitochondrial genome. Position Gene/elements
Origin
Stop
Size (bp)
Phe
1 71 1037 1107 2706 2782 3753 3822 3892 3961 5003 5079 5149 5223 5248 5314 5386 6925 6998 7068 7756 7830 7988 8671 9455 9524 9873 9943 10,236 11,626 11,696 11,761 11,833 13,634 14,159 14,231 15,375 15,448 15,517
72 1036 1106 2705 2781 3750 3822 3892 3960 5002 5077 5147 5221 5250 5313 5384 6933 6995 7067 7754 7828 7997 8671 9454 9523 9872 9942 10,242 11,612 11,695 11,761 11,832 13,638 14,158 14,226 15,370 15,446 15,516 16,489
70 966 70 1599 76 969 70 71 69 1042 75 69 73 28 66 71 1548 71 70 687 73 168 684 784 69 351 70 300 1377 70 66 72 1806 525 68 1150 72 69 973
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1 tRNASer(UCN) tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro Control region
Strand (sense) H H H H H H H L H H H L 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 H
Codon Start
Stop
ATG
TAA
ATG
T– –
ATG
AGG
ATG
TAA
ATG ATG ATG
TAA TAA T– –
ATG
T– –
ATG ATG
TAA TAA
ATG ATG
TAA AGG
ATG
T– –
Downloaded by [Chinese University of Hong Kong] at 00:49 07 November 2015
2
Q.-Y. Jiang et al.
reflects a typical sequence feature of the vertebrate mitochondrial genome. ND2 gene started with ATT, the start codon of ND3 was ATA, other 11 protein-coding genes started with ATG. ND2, ND3, ND4, COX3 and Cyt b genes had incomplete stop codons of T, ND1 gene end with TAG, ND6 gene was terminated with AGA, the stop codons of the rest protein-coding genes were TAA. The length of 12SrRNA gene was 948 bp and 16SrRNA gene was 1562 bp, 2 genes were separated by the tRNAVal and positioned between the tRNAPhe and tRNALeu(UUR). The 22 tRNA genes ranged in size from 59 bp to 75 bp, which were typical animal mtDNA genes, could be folded into the analogous cloverleaf secondly structure. The light-strand replication origin (OL) positioned in the WANCY tRNA genes cluster and located between tRNAAsn and tRNACys, it might potentially fold into a stable stem-loop secondary structure with a stem comprised of 10 bp and a loop of 12 nucleotides. The length of control region (D-Loop) was 1093 bp, 57.64% A + T rich and flanked by tRNAPro and tRNAPhe genes.
Declaration of interest This article is original, has been written by the stated authors who are all aware of its content and approve its submission, has not been published
Mitochondrial DNA, Early Online: 1–2
previously, it is not under consideration for publication elsewhere, no conflict of interest exists, and if accepted, the article will not be published elsewhere in the same form, in any language, without the written consent of the publisher. This research was partially funded by National Natural Science Foundation of China (81360135) and the Natural Science Foundation of Guangxi province (2012GXNSFBA053041, 2013GXNSFAA019187).
References Bleisch B, Ha MN, Quyet KL, Yongcheng L. (2008). Trachypithecus francoisi. In: IUCN 2013. IUCN Red List of Threatened Species. Version 2013.2. Available at: http://www.iucnredlist.org (Accessed 12 May 2014). Liu ZJ, Wang BS, Nadler T, Liu GJ, Sun T, Huang CM, Zhou QH, et al. (2013). Relatively recent evolution of pelage coloration in Colobinae: Phylogeny and phylogeography of three closely related langur species. PLoS One 8:e61659. Wang SL, Luo Y, Cui GF. (2011). Sleeping site selection of Francois’s langur (Trachypithecus francoisi) in two habitats in Mayanghe National Nature Reserve, Guizhou, China. Primates 52: 51–60. Zeng YJ, Xu JL, Wang Y, Zhou CF. (2013). Habitat association and conservation implications of Endangered Francois’ Langur (Trachypithecus francoisi). PLoS One 8:e75661.
