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 cristatus Qin-yang Jiang & Yan-na Huang To cite this article: Qin-yang Jiang & Yan-na Huang (2016) Complete mitochondrial genome of the Trachypithecus cristatus, Mitochondrial DNA, 27:2, 1101-1102, DOI: 10.3109/19401736.2014.930841 To link to this article: http://dx.doi.org/10.3109/19401736.2014.930841
Published online: 30 Jun 2014.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Gazi University]
Date: 16 January 2016, At: 14:33
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2016; 27(2): 1101–1102 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.930841
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the Trachypithecus cristatus Qin-yang Jiang and Yan-na Huang
Downloaded by [Gazi University] at 14:33 16 January 2016
College of animal science and technology, Guangxi University, Nanning, China
Abstract
Keywords
In this study, the complete mitochondrial genome of Trachypithecus cristatus was determined using PCR method. The mitochondrial genome is 16,557 bp in length, it containing 13 proteincoding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The structural organization and gene order of T. cristatus mtDNA were similar to that of most other vertebrates. The results could provide useful information for further studies on phylogenetics of T. cristatus.
Mitochondrial genome, structural organization, trachypithecus cristatus
The Trachypithecus cristatus is a medium sized monkey with a long, non-prehensile tail. Its pelage color and hairs are grayish white and lighter distally, giving a silvered appearance, hence names as Silvery Lutung, Silvered Leaf monkey or Silvered Langur (Harding, 2010). T. cristatus is wide distribution in the mainland Southeast Asia, including Thailand, Cambodia, Myanmar, Laos, Vietnam, and southern Malaysian peninsula (Fan et al., 2013; Roos et al., 2008). It is a folivorous species and living in variety forests (Harding, 2010). T. cristatus is heavily threatened by logging and plantations development, hunting for meat and medicinal, and capture for pet trade (Geissmann et al., 2006). It is now listed as Near Threatened by the IUCN (Nijman & Meijaard, 2008), and is included on Appendix II of CITES (2013). In this paper, a frozen blood sample of adult female T. cristatus was provided by Nanning Zoo in Guangxi province, China. The blood total DNA was extracted by traditional phenol/chloroform method. The fragments of T. cristatus mitochondrial DNA (mtDNA) were amplified by polymerase chain reaction method with 17 pairs of primers, with each fragment sequence overlapping the next by over 100 bp. Seventeen PCR products were purified, and were sequenced directly by the primer walking method, respectively. Each fragment was sequenced more than three copies to ensure the reliability of the data. We used the DNAstar Lasergene 7.0 software (Madison, WI) to analyze sequenced data and assemble contigs into a continuous sequence. The locations of protein-coding gene, 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 monkey mitochondrial genome. The mitochondrial genome of T. cristatus was 16,557 bp in length, it was firstly sequenced and has been deposited in GenBank (Accession No. KJ174503). In the overall base composition of the T. cristatus mtDNA was A ¼ 32.22%, Correspondence: Yan-Na Huang, College of animal science and technology, Guangxi University, Nanning, Guangxi Province 530004, PR China. Tel/Fax: +86 771 3235635. E-mail: [email protected]
History Received 31 May 2014 Accepted 1 June 2014 Published online 26 June 2014
T ¼ 28.77%, C ¼ 26.29% and G ¼ 12.72%. This A + T rich pattern reflected a typical sequence feature of the animal mitochondrial genome. The structural organization and gene order of the complete mitochondrial DNA of T. cristatus was identical that of other typical vertebrate, with the mitochondrial genome containing the following (Table 1): 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region (D-Loop). The start codons of ND2 and ND3 genes were ATT, other 11 proteinTable 1. The structural organization of the T. cristatus mitochondrial genome. Position Gene/elements Phe
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
Origin 1 72 1020 1089 2654 2731 3686 3824 3826 3894 4936 5081 5155 5189 5253 5318 5329 6939 6943 7012 7743 7811 7972 8652 9436
Codon
Stop
Size (bp)
Strand (sense)
71 1019 1088 2653 2728 3685 3755 3753 3893 4935 5004 5013 5083 5157 5188 5253 6873 6871 7010 7695 7809 8017 8652 9435 9503
71 948 69 1564 75 954 70 72 68 1044 69 69 73 33 66 66 1545 69 68 684 67 207 681 784 68
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
Start
Stop
ATG
T– –
ATT
T– –
ATG
TAA
ATG
TAG
ATG ATG ATG
TAA TAA T– –
(continued )
1102
Q.-Y. Jiang & Y.-N. Huang
Mitochondrial DNA, 2016; 27(2): 1101–1102
Table 1. Continued
Downloaded by [Gazi University] at 14:33 16 January 2016
Position
Codon
Gene/elements
Origin
Stop
Size (bp)
Strand (sense)
ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro Control region
9504 9850 9915 10,205 11,583 11,652 11,711 11,786 141,16 14,185 14,190 15,331 15,465 15,466
9849 9914 10,211 11,582 11,651 11,710 11,781 13,591 13,592 14,117 15,330 15,395 15,398 16,557
346 65 297 1378 69 59 71 1806 525 69 1141 65 68 1092
H H H H H H H H L L H H L H
Start
Stop
ATT
T– –
ATG ATG
TAA T– –
ATG ATG
TAA AGA
ATG
T– –
cluster and located between tRNAAsn and tRNACys, it might potentially fold into a stable stem-loop secondary structure with a stem comprised of 9 bp and a loop of 15 nucleotides. The length of control region (D-Loop) was 1092 bp, 58.06% A + T rich and flanked by tRNAPro and tRNAPhe genes.
Declaration of interest
coding genes started with ATG. ND1 4, COX3 and Cytb genes had incomplete stop codons of T, COX2 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 1564 bp, two genes were separated by the tRNAVal and positioned between the tRNAPhe and tRNALeu(UUR). 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
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 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 the Natural Science Foundation of Guangxi province (2012GXNSFBA053041, 2013GXNSFAA019187).
References Fan XB, Krit P, Hasmik M, Pornnarong S, Nadezda K, Weerayuth S, Alongkoad T, et al. (2013). First detailed reconstruction of the karyotype of Trachypithecus cristatus (Mammalia: Cercopithecidae). Mol Cytogenet 6:58–66. Geissmann T, Nijman V, Dallmann R. (2006). The fate of diurnal primates in southern Sumatra. Gibbon J 2:18–24. Harding LE. (2010). Trachypithecus cristatus (Primates: Cercopithecidae). Mamm Species 42:149–65. Nijman V, Meijaard E. (2008). Trachypithecus cristatus. In: IUCN 2013. IUCN Red Listof Threatened Species. Version 2013.2. Available: www.iucnredlist.org (Accessed 13 May 2014) Roos C, Nadler T, Walter L. (2008). Mitochondrial phylogeny, taxonomy and biogeography of the silvered langur species group (Trachypithecus cristatus). Mol Phylogenet Evol 47:629–36.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of the Trachypithecus cristatus Qin-yang Jiang & Yan-na Huang To cite this article: Qin-yang Jiang & Yan-na Huang (2016) Complete mitochondrial genome of the Trachypithecus cristatus, Mitochondrial DNA, 27:2, 1101-1102, DOI: 10.3109/19401736.2014.930841 To link to this article: http://dx.doi.org/10.3109/19401736.2014.930841
Published online: 30 Jun 2014.
Submit your article to this journal
Article views: 11
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: [Gazi University]
Date: 16 January 2016, At: 14:33
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2016; 27(2): 1101–1102 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.930841
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the Trachypithecus cristatus Qin-yang Jiang and Yan-na Huang
Downloaded by [Gazi University] at 14:33 16 January 2016
College of animal science and technology, Guangxi University, Nanning, China
Abstract
Keywords
In this study, the complete mitochondrial genome of Trachypithecus cristatus was determined using PCR method. The mitochondrial genome is 16,557 bp in length, it containing 13 proteincoding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The structural organization and gene order of T. cristatus mtDNA were similar to that of most other vertebrates. The results could provide useful information for further studies on phylogenetics of T. cristatus.
Mitochondrial genome, structural organization, trachypithecus cristatus
The Trachypithecus cristatus is a medium sized monkey with a long, non-prehensile tail. Its pelage color and hairs are grayish white and lighter distally, giving a silvered appearance, hence names as Silvery Lutung, Silvered Leaf monkey or Silvered Langur (Harding, 2010). T. cristatus is wide distribution in the mainland Southeast Asia, including Thailand, Cambodia, Myanmar, Laos, Vietnam, and southern Malaysian peninsula (Fan et al., 2013; Roos et al., 2008). It is a folivorous species and living in variety forests (Harding, 2010). T. cristatus is heavily threatened by logging and plantations development, hunting for meat and medicinal, and capture for pet trade (Geissmann et al., 2006). It is now listed as Near Threatened by the IUCN (Nijman & Meijaard, 2008), and is included on Appendix II of CITES (2013). In this paper, a frozen blood sample of adult female T. cristatus was provided by Nanning Zoo in Guangxi province, China. The blood total DNA was extracted by traditional phenol/chloroform method. The fragments of T. cristatus mitochondrial DNA (mtDNA) were amplified by polymerase chain reaction method with 17 pairs of primers, with each fragment sequence overlapping the next by over 100 bp. Seventeen PCR products were purified, and were sequenced directly by the primer walking method, respectively. Each fragment was sequenced more than three copies to ensure the reliability of the data. We used the DNAstar Lasergene 7.0 software (Madison, WI) to analyze sequenced data and assemble contigs into a continuous sequence. The locations of protein-coding gene, 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 monkey mitochondrial genome. The mitochondrial genome of T. cristatus was 16,557 bp in length, it was firstly sequenced and has been deposited in GenBank (Accession No. KJ174503). In the overall base composition of the T. cristatus mtDNA was A ¼ 32.22%, Correspondence: Yan-Na Huang, College of animal science and technology, Guangxi University, Nanning, Guangxi Province 530004, PR China. Tel/Fax: +86 771 3235635. E-mail: [email protected]
History Received 31 May 2014 Accepted 1 June 2014 Published online 26 June 2014
T ¼ 28.77%, C ¼ 26.29% and G ¼ 12.72%. This A + T rich pattern reflected a typical sequence feature of the animal mitochondrial genome. The structural organization and gene order of the complete mitochondrial DNA of T. cristatus was identical that of other typical vertebrate, with the mitochondrial genome containing the following (Table 1): 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region (D-Loop). The start codons of ND2 and ND3 genes were ATT, other 11 proteinTable 1. The structural organization of the T. cristatus mitochondrial genome. Position Gene/elements Phe
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
Origin 1 72 1020 1089 2654 2731 3686 3824 3826 3894 4936 5081 5155 5189 5253 5318 5329 6939 6943 7012 7743 7811 7972 8652 9436
Codon
Stop
Size (bp)
Strand (sense)
71 1019 1088 2653 2728 3685 3755 3753 3893 4935 5004 5013 5083 5157 5188 5253 6873 6871 7010 7695 7809 8017 8652 9435 9503
71 948 69 1564 75 954 70 72 68 1044 69 69 73 33 66 66 1545 69 68 684 67 207 681 784 68
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
Start
Stop
ATG
T– –
ATT
T– –
ATG
TAA
ATG
TAG
ATG ATG ATG
TAA TAA T– –
(continued )
1102
Q.-Y. Jiang & Y.-N. Huang
Mitochondrial DNA, 2016; 27(2): 1101–1102
Table 1. Continued
Downloaded by [Gazi University] at 14:33 16 January 2016
Position
Codon
Gene/elements
Origin
Stop
Size (bp)
Strand (sense)
ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro Control region
9504 9850 9915 10,205 11,583 11,652 11,711 11,786 141,16 14,185 14,190 15,331 15,465 15,466
9849 9914 10,211 11,582 11,651 11,710 11,781 13,591 13,592 14,117 15,330 15,395 15,398 16,557
346 65 297 1378 69 59 71 1806 525 69 1141 65 68 1092
H H H H H H H H L L H H L H
Start
Stop
ATT
T– –
ATG ATG
TAA T– –
ATG ATG
TAA AGA
ATG
T– –
cluster and located between tRNAAsn and tRNACys, it might potentially fold into a stable stem-loop secondary structure with a stem comprised of 9 bp and a loop of 15 nucleotides. The length of control region (D-Loop) was 1092 bp, 58.06% A + T rich and flanked by tRNAPro and tRNAPhe genes.
Declaration of interest
coding genes started with ATG. ND1 4, COX3 and Cytb genes had incomplete stop codons of T, COX2 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 1564 bp, two genes were separated by the tRNAVal and positioned between the tRNAPhe and tRNALeu(UUR). 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
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 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 the Natural Science Foundation of Guangxi province (2012GXNSFBA053041, 2013GXNSFAA019187).
References Fan XB, Krit P, Hasmik M, Pornnarong S, Nadezda K, Weerayuth S, Alongkoad T, et al. (2013). First detailed reconstruction of the karyotype of Trachypithecus cristatus (Mammalia: Cercopithecidae). Mol Cytogenet 6:58–66. Geissmann T, Nijman V, Dallmann R. (2006). The fate of diurnal primates in southern Sumatra. Gibbon J 2:18–24. Harding LE. (2010). Trachypithecus cristatus (Primates: Cercopithecidae). Mamm Species 42:149–65. Nijman V, Meijaard E. (2008). Trachypithecus cristatus. In: IUCN 2013. IUCN Red Listof Threatened Species. Version 2013.2. Available: www.iucnredlist.org (Accessed 13 May 2014) Roos C, Nadler T, Walter L. (2008). Mitochondrial phylogeny, taxonomy and biogeography of the silvered langur species group (Trachypithecus cristatus). Mol Phylogenet Evol 47:629–36.
