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 Stumptailed Macaques (Macaca arctoides) Zongtao Liu, Yaoyao Cui, Jianqiu Yu, Lili Niu, Jiabo Deng, Juan Jiang & Jing Li To cite this article: Zongtao Liu, Yaoyao Cui, Jianqiu Yu, Lili Niu, Jiabo Deng, Juan Jiang & Jing Li (2014): The complete mitochondrial genome of Stump-tailed Macaques (Macaca arctoides), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.961149
Published online: 22 Sep 2014.
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Date: 05 November 2015, At: 17:40
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.961149
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Stump-tailed Macaques (Macaca arctoides) Zongtao Liu1*, Yaoyao Cui1*, Jianqiu Yu2, Lili Niu2, Jiabo Deng2, Juan Jiang1, and Jing Li1 1
Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China and Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu, P.R. China
Downloaded by [University of California, San Diego] at 17:40 05 November 2015
2
Abstract
Keywords
Stump-tailed macaque (Macaca arctoides) has been enlisted as the Near Threatened species in the IUCN Red List. In this study, the complete mitochondial genome of M. arctoides was determined. The mitogenome was 16,559 bp in length with an A + T content of 56.8%, containing 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), 13 protein-coding genes (PCGs) and a control region (D-loop). Ten protein-coding genes (ND1, COX1, COX2, ND4, COX3, ND4L, ATP8, ATP6, CYTB, ND6) started with ATG codons, while ND2, ND3 and ND5 initiated with ATT, ATC and ATA, respectively. Eight PCGs ended with complete termination codons except for COX3, ND3, ND4, and CYTB terminated with incompleted codon T.
Genome structure, Macaca arctoides, mitochondial genome
Stump-tailed macaques (Macaca arctoides), belonging to genus Macaca, family Cercopithecidae, Old World monkeys (OWM) lineage, mainly occur in Cambodia, south-western China, northeastern India, Lao PDR, north-western Peninsular Malaysia, northern Myanmar, Thailand, and Vietnam. To date, the phylogenetic position of M. arctoides remains to be controversial in genus Macaca based on different molecular markers (Morales & Melnick, 1998; Li et al., 2009; Tosi et al., 2000). Now, we sequenced the complete mitochondrial genome of M. arctoides (GenBank accession no. KM360179), which will be undoubted
History Received 25 August 2014 Accepted 31 August 2014 Published online 22 September 2014
benefit of the phylogentic study as well as the conservation management of M. arctoides in the future. The blood sample from a female stump-tailed macaque was obtained from Chengdu Zoo, Sichuan Province, China. Total genome DNA was extracted according to the method of Sambrook & Russell (2001). In this study, fourteen primer sets were designed on the basis of the converved sequences of five specise of genus Macaca: M. mulatta (NC_005943), M. sylvanus (NC_002764), M. thibetana (NC_011519) and M. fascicularis (NC_012670), M. assamensis (NC_023795.1). The complete
Table 1. Complete mitochondrial genome of M. arctoides. Gene Control region tRNA-Phe s-rRNA tRNA-Val l-rRNA tRNA-Leu(UUR) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn OL tRNA-Cys tRNA-Tyr COX1
Start position
Stop position
Intergenic spacer
16,006.1 530 602 1553 1622 3186 3263 4218 4284 4355 4423 5465 5539 5609 5683 5714 5782 5852
16,559.529 601 1552 1621 3185 3260 4219 4286 4354 4422 5466 5531 5607 5681 5715 5776 5847 7390
0 0 0 0 0 2 –2 –3 0 0 –2 7 1 1 –2 5 4 2
Start codon
End codon
ATG
TAG
ATT
TAG
ATG
Size(bp)
Stand(sense)
1083 72 951 69 1564 75 957 69 71 68 1044 67 69 73 33 63 66 1539
H H H H H H H H L H H H L L L L L H (continued )
*These authors contributed equally to the work. Correspondence: Jing Li, Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China. E-mail: [email protected]
2
Z. Liu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Downloaded by [University of California, San Diego] at 17:40 05 November 2015
Gene tRNA-Ser(UCN) tRNA-Asp COX2 tRNA-Lys ATP8 ATP6 COX3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser(AGY) tRNA-Leu(CUN) ND5 ND6 tRNA-Glu CYTB tRNA-Thr tRNA-Pro
Start position 7393 7465 7534 8281 8348 8509 9189 9973 10,041 10,387 10,452 10,742 12,120 12,189 12,248 12,319 14,131 14,659 14,732 15,873 15,938
Stop position 7461 7532 8217 8346 8554 9189 9972 10,040 10,386 10,451 10,748 12,119 12,188 12,247 12,318 14,130 14,658 14,727 15,872 15,936 16,005
Intergenic spacer 3 1 63 1 –46 –1 0 0 0 0 –7 0 0 0 0 0 0 4 0 1 0
mitogenome of M. arctoides is 16,559 bp in length, consisting of 13 protein-coding genes (PCGs), 2 rRNA, 22 tRNA and a displacement loop (D-loop) locus (Table 1). The nucleotide composition is 32.0% A, 24.8% T, 30.5% C and 12.7% G. The A + T content is 56.8%, which corresponds well to the percentage found in the mtDNA of vertebrate mitochondrial genome (Zhang et al., 2003). Among 13 protein-coding genes (PCGs), the lowest A + T content was 54.0% in CYTB and the highest was 60.4% in ATP8. All PCGs were encoded on the heavy strand (H strand) except for the ND6 gene. Ten PCGs (ND1, COX1, COX2, ND4, COX3, ND4L, ATP8, ATP6, ND6, CYTB) started with ATG initiation codon, whereas ND2, ND3 and ND5 initiated with ATT, ATC and ATA, respectively. In mammals, the commonly used initiation codons were ATG and ATA (Xu & Arnason, 1994). Five PCGs (ND5, ND4L, ATP6, COX2, ATP8) harbored the typical termination codon TAA, two genes (ND1, ND2) end with TAG, one gene (ND6) terminated with AGG, while four genes (ND3, ND4, COX3, CYTB) ended in incomplete codon T, which may be completed by post-transcriptional polyadenylation as TAA (Anderson et al., 1981). In our study, the COX1 gene stop codon was still not determined with the same situation found in previous sequenced Cercopithecinae species. The length of two subunits of rRNA (s-rRNA and l-rRNA) were 951 bp and 1564 bp, respectively, with an overall A + T composition of 56.7%. The 22 tRNA genes with in size ranging from 59 to 73 bp, could be folded into the typical cloverleaf secondary structure with the exception of tRNA-ser (AGY) with the ‘‘DHU’’ arm deletion as the same case in other genus Macaca. The control region was 1083 bp long, located between tRNA-Pro and tRNA-Phe. The origin of L-strand replication (OL) was 33 bp
Start codon
End codon
ATG
TAA
ATG ATG ATG
TAA TAA T
ATC
T
ATG ATG
TAA T
ATA ATG
TAA AGG
ATG
T
Size(bp)
Stand(sense)
69 68 684 66 207 681 784 68 346 65 297 1378 69 59 71 1812 528 69 1141 64 68
L H H H H H H H H H H H H H H H L L H H L
which shared AA basic group with the tRNA-Cys gene, eighteen basic group can be folded nine base-pairs located on the stem.
Declaration of interest This research was funded by the National Natural Science Foundation of China (No. 31270431), and partial by the Scientific Research Foundation for the Returned Overseas Scholars, State Education Ministry (201115688-3), and the Sichuan University Youth Science and Technology Foundation. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, et al. (1981). Sequence and organization of the human mitochondrial genome. Nature 290:457–64. Li J, Han K, Xing JC, Kim HS, Rogers J, Ryder OA, Disotell T, et al. (2009). Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. Gene 448:242–9. Morales JC, Melnick DJ. (1998). Phylogenetic relationships of the macaques (Cercopithecidae: Macaca), as revealed by high resolution restriction site mapping of mitochondrial ribosomal genes. J Hum Evol 34:1–23. Sambrook J, Russell DW. (2001). Molecular cloning: A laboratory manual. Cold Spring Harbor, NY: Cold Spring Harbor Press. Tosi AJ, Morales JC, Melnick DJ. (2000). Comparison of Y chromosome and mtDNA phylogenies leads to unique inferences of macaque evolutionary history. Mol Phylogenet Evol 17:133–44. Xu X, Arnason U. (1994). The complete mitochondrial DNA sequence of the horse, Equcaballus: Extensive heteroplasmy of the control region. Gene 148:357–62. Zhang P, Chen YQ, Liu YF, Zhou H, Qu LH. (2003). The complete mitochondrial genome of the Chinese giant salamander, Andrias davidianus (Amphibia: Caudata). Gene 311:93–8.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Stumptailed Macaques (Macaca arctoides) Zongtao Liu, Yaoyao Cui, Jianqiu Yu, Lili Niu, Jiabo Deng, Juan Jiang & Jing Li To cite this article: Zongtao Liu, Yaoyao Cui, Jianqiu Yu, Lili Niu, Jiabo Deng, Juan Jiang & Jing Li (2014): The complete mitochondrial genome of Stump-tailed Macaques (Macaca arctoides), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.961149
Published online: 22 Sep 2014.
Submit your article to this journal
Article views: 20
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: [University of California, San Diego]
Date: 05 November 2015, At: 17:40
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.961149
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Stump-tailed Macaques (Macaca arctoides) Zongtao Liu1*, Yaoyao Cui1*, Jianqiu Yu2, Lili Niu2, Jiabo Deng2, Juan Jiang1, and Jing Li1 1
Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China and Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu, P.R. China
Downloaded by [University of California, San Diego] at 17:40 05 November 2015
2
Abstract
Keywords
Stump-tailed macaque (Macaca arctoides) has been enlisted as the Near Threatened species in the IUCN Red List. In this study, the complete mitochondial genome of M. arctoides was determined. The mitogenome was 16,559 bp in length with an A + T content of 56.8%, containing 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), 13 protein-coding genes (PCGs) and a control region (D-loop). Ten protein-coding genes (ND1, COX1, COX2, ND4, COX3, ND4L, ATP8, ATP6, CYTB, ND6) started with ATG codons, while ND2, ND3 and ND5 initiated with ATT, ATC and ATA, respectively. Eight PCGs ended with complete termination codons except for COX3, ND3, ND4, and CYTB terminated with incompleted codon T.
Genome structure, Macaca arctoides, mitochondial genome
Stump-tailed macaques (Macaca arctoides), belonging to genus Macaca, family Cercopithecidae, Old World monkeys (OWM) lineage, mainly occur in Cambodia, south-western China, northeastern India, Lao PDR, north-western Peninsular Malaysia, northern Myanmar, Thailand, and Vietnam. To date, the phylogenetic position of M. arctoides remains to be controversial in genus Macaca based on different molecular markers (Morales & Melnick, 1998; Li et al., 2009; Tosi et al., 2000). Now, we sequenced the complete mitochondrial genome of M. arctoides (GenBank accession no. KM360179), which will be undoubted
History Received 25 August 2014 Accepted 31 August 2014 Published online 22 September 2014
benefit of the phylogentic study as well as the conservation management of M. arctoides in the future. The blood sample from a female stump-tailed macaque was obtained from Chengdu Zoo, Sichuan Province, China. Total genome DNA was extracted according to the method of Sambrook & Russell (2001). In this study, fourteen primer sets were designed on the basis of the converved sequences of five specise of genus Macaca: M. mulatta (NC_005943), M. sylvanus (NC_002764), M. thibetana (NC_011519) and M. fascicularis (NC_012670), M. assamensis (NC_023795.1). The complete
Table 1. Complete mitochondrial genome of M. arctoides. Gene Control region tRNA-Phe s-rRNA tRNA-Val l-rRNA tRNA-Leu(UUR) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn OL tRNA-Cys tRNA-Tyr COX1
Start position
Stop position
Intergenic spacer
16,006.1 530 602 1553 1622 3186 3263 4218 4284 4355 4423 5465 5539 5609 5683 5714 5782 5852
16,559.529 601 1552 1621 3185 3260 4219 4286 4354 4422 5466 5531 5607 5681 5715 5776 5847 7390
0 0 0 0 0 2 –2 –3 0 0 –2 7 1 1 –2 5 4 2
Start codon
End codon
ATG
TAG
ATT
TAG
ATG
Size(bp)
Stand(sense)
1083 72 951 69 1564 75 957 69 71 68 1044 67 69 73 33 63 66 1539
H H H H H H H H L H H H L L L L L H (continued )
*These authors contributed equally to the work. Correspondence: Jing Li, Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China. E-mail: [email protected]
2
Z. Liu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Downloaded by [University of California, San Diego] at 17:40 05 November 2015
Gene tRNA-Ser(UCN) tRNA-Asp COX2 tRNA-Lys ATP8 ATP6 COX3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser(AGY) tRNA-Leu(CUN) ND5 ND6 tRNA-Glu CYTB tRNA-Thr tRNA-Pro
Start position 7393 7465 7534 8281 8348 8509 9189 9973 10,041 10,387 10,452 10,742 12,120 12,189 12,248 12,319 14,131 14,659 14,732 15,873 15,938
Stop position 7461 7532 8217 8346 8554 9189 9972 10,040 10,386 10,451 10,748 12,119 12,188 12,247 12,318 14,130 14,658 14,727 15,872 15,936 16,005
Intergenic spacer 3 1 63 1 –46 –1 0 0 0 0 –7 0 0 0 0 0 0 4 0 1 0
mitogenome of M. arctoides is 16,559 bp in length, consisting of 13 protein-coding genes (PCGs), 2 rRNA, 22 tRNA and a displacement loop (D-loop) locus (Table 1). The nucleotide composition is 32.0% A, 24.8% T, 30.5% C and 12.7% G. The A + T content is 56.8%, which corresponds well to the percentage found in the mtDNA of vertebrate mitochondrial genome (Zhang et al., 2003). Among 13 protein-coding genes (PCGs), the lowest A + T content was 54.0% in CYTB and the highest was 60.4% in ATP8. All PCGs were encoded on the heavy strand (H strand) except for the ND6 gene. Ten PCGs (ND1, COX1, COX2, ND4, COX3, ND4L, ATP8, ATP6, ND6, CYTB) started with ATG initiation codon, whereas ND2, ND3 and ND5 initiated with ATT, ATC and ATA, respectively. In mammals, the commonly used initiation codons were ATG and ATA (Xu & Arnason, 1994). Five PCGs (ND5, ND4L, ATP6, COX2, ATP8) harbored the typical termination codon TAA, two genes (ND1, ND2) end with TAG, one gene (ND6) terminated with AGG, while four genes (ND3, ND4, COX3, CYTB) ended in incomplete codon T, which may be completed by post-transcriptional polyadenylation as TAA (Anderson et al., 1981). In our study, the COX1 gene stop codon was still not determined with the same situation found in previous sequenced Cercopithecinae species. The length of two subunits of rRNA (s-rRNA and l-rRNA) were 951 bp and 1564 bp, respectively, with an overall A + T composition of 56.7%. The 22 tRNA genes with in size ranging from 59 to 73 bp, could be folded into the typical cloverleaf secondary structure with the exception of tRNA-ser (AGY) with the ‘‘DHU’’ arm deletion as the same case in other genus Macaca. The control region was 1083 bp long, located between tRNA-Pro and tRNA-Phe. The origin of L-strand replication (OL) was 33 bp
Start codon
End codon
ATG
TAA
ATG ATG ATG
TAA TAA T
ATC
T
ATG ATG
TAA T
ATA ATG
TAA AGG
ATG
T
Size(bp)
Stand(sense)
69 68 684 66 207 681 784 68 346 65 297 1378 69 59 71 1812 528 69 1141 64 68
L H H H H H H H H H H H H H H H L L H H L
which shared AA basic group with the tRNA-Cys gene, eighteen basic group can be folded nine base-pairs located on the stem.
Declaration of interest This research was funded by the National Natural Science Foundation of China (No. 31270431), and partial by the Scientific Research Foundation for the Returned Overseas Scholars, State Education Ministry (201115688-3), and the Sichuan University Youth Science and Technology Foundation. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, et al. (1981). Sequence and organization of the human mitochondrial genome. Nature 290:457–64. Li J, Han K, Xing JC, Kim HS, Rogers J, Ryder OA, Disotell T, et al. (2009). Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. Gene 448:242–9. Morales JC, Melnick DJ. (1998). Phylogenetic relationships of the macaques (Cercopithecidae: Macaca), as revealed by high resolution restriction site mapping of mitochondrial ribosomal genes. J Hum Evol 34:1–23. Sambrook J, Russell DW. (2001). Molecular cloning: A laboratory manual. Cold Spring Harbor, NY: Cold Spring Harbor Press. Tosi AJ, Morales JC, Melnick DJ. (2000). Comparison of Y chromosome and mtDNA phylogenies leads to unique inferences of macaque evolutionary history. Mol Phylogenet Evol 17:133–44. Xu X, Arnason U. (1994). The complete mitochondrial DNA sequence of the horse, Equcaballus: Extensive heteroplasmy of the control region. Gene 148:357–62. Zhang P, Chen YQ, Liu YF, Zhou H, Qu LH. (2003). The complete mitochondrial genome of the Chinese giant salamander, Andrias davidianus (Amphibia: Caudata). Gene 311:93–8.
