http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1025265
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Southern pig-tailed macaque, Macaca nemestrina, and comparative mitochondrial genomics of Macaca species Chen Chen1, Huixian Mei2, and Xueting Luo1
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/30/15 For personal use only.
1
Clinical School of University of Hubei Chinese Medicine, Wuhan, Hubei, China and 2Physical Culture of Institute of Hubei University, Wuhan, Hubei, China Abstract
Keywords
In this study, we report the complete mitochondrial genome sequence of Southern pig-tailed, Macaca nemestrina for the first time. The genome is found to be 16,560 bp in length and has a base composition of A (32.25%), G (12.31%), C (30.51%), and T (24.93%), indicating that the percentage of A + T (57.18%) was higher than G + C (42.82%). Similar to other monkeys, it contains a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Most of the genes were located on the H-strand except for the ND6 gene and 8 tRNA genes. To obtain a more complete understanding of the evolutionary history of Macaca genus, 11 mitochondrial genomes were used for phylogenetic analysis. This mitochondrial sequence reported here would be useful to uncover the monkey’s evolution and add a new genetic resource for the genus Macaca.
Macaca nemestrina, mitochondrial genome, phylogenetic analysis
The Southern pig-tailed macaque, Macaca nemestrina, is a medium-sized primate with light brown fur, which is found in a portion of Southeast Asia from southern Thailand to the island of Borneo (Richardson et al., 2008). It is a species of genus Macaca. To date, more than 20 different species were recognized in the genus of Macaca (Fooden, 1976). Here, using the CLC Genomic Workbench v3.6 (2010), we assembled and analyzed the mitochondrial genome of Southern pig-tailed macaque, Macaca nemestrina. The blood sample was obtained from an individual and total genomic DNA was extracted and sequenced. We downloaded the genome raw reads, which were sequenced by Illumina HiSeq 2000, from NCBI (http://www.ncbi.nlm.nih.gov/ sra/). This mitochondrial sequence reported here would be useful to uncover the monkey’s evolution and add a new genetic resource for the genus Macaca. The complete mitogenome of M. nemestrina was 16,560 bp in length (GenBank accession No. KP765688). It harbored a total of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12 S rRNA and 16 S rRNA) and 1 non-coding control region (D-loop). Most of these genes were located on the H-strand except for the ND6 subunit gene and 8 tRNA genes, which were encoded on the L-strand. The arrangement of all genes did not differ significantly in comparison with other monkeys (Horai et al., 1992; Li et al., 2009; Wang et al., 2014). The overall base composition was 32.25% of A, 24.93% of T, 30.51% of C, and 12.31% of G, so the percentage of A and T (57.18%) was slightly higher than that of G and C (42.82%).
History Received 12 February 2015 Accepted 28 February 2015 Published online 22 May 2015
The total length of the 13 identified protein-coding genes was 11,355 bp, and they encoded 3791 amino acids in all. The 22 tRNA genes of M. nemestrina, ranging from 59 bp (tRNA-Ser) to 75 bp (tRNA-Leu), were determined based on their respective anticodons and secondary structures. The control region (CR) or D-loop region of the Southern pig-tailed macaque is located between tRNA-Pro and tRNA-Phe, and is 1082 bp. The total length of 12 S rRNA gene and 16 S rRNA gene is 948 bp and 1561 bp, respectively. To obtain a more complete understanding of the evolutionary history of Macaca genus, 11 mitochondrial genomes were used for phylogenetic analysis. Multiple alignments of these fragments were performed using MUSCLE (Edgar, 2004) with the default settings. The complete mitochondrial genome sequences of 10 other Macaca species are available from GenBank and the names of these species are as follows: M. arctoides, M. assamensis, M. fascicularis, M. fuscata, M. mulatta, M. silenus, M. sylvanus, M. thibetana, M. nigra, M. tonkeana (Arnason et al., 2001; Gokey et al., 2004; Li et al., 2009; Wang et al., 2014). The phylogenetic tree from maximum-likelihood (ML) was reconstructed using the MEGA5 (Tamura et al., 2011). Our analysis revealed three major clades within the Macaca (Figure 1), and one clade consists of M. nemestrina and three macaques. In this clade M. mulatta and M. fuscata formed a sister group to M. nigra, then grouped with M. nemestrina, which suggests that M. nemestrina emerged earlier than M. mulatta and M. fuscata. The other two clades consist of 4 species and 3 species, respectively.
Correspondence: Xueting Luo, Clinical School of University of Hubei Chinese Medicine, Wuhan, Hubei, China. Tel/Fax: +86-027-68889091. E-mail: [email protected]
2
C. Chen et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/30/15 For personal use only.
Figure 1. Phylogeny based on mtDNA sequences. The maximum-likelihood tree is drawn to scale. Mt genome size and AT content shown for each species. The NCBI accession number corresponds to each sequence.
Acknowledgements We would like to thank anonymous reviewers for providing valuable comments on the manuscript.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Arnason U, Gullberg A, Burguete AS, Janice A. (2001). Molecular estimates of primate divergences and new hypotheses for primate dispersal and the origin of modern humans. Hereditas 133:217–28. CLC Genomics Workbench v3.6. (2010). Available at: http:// www.clcbio.com/products/clc-genomics-workbench/ (Accessed 11 March 2015). Edgar RC. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–7. Fooden J. (1976). Provisional classification and key to living species of macaques (Primates: Macaca). Folia Primatol 25:225–36.
Gokey NG, Cao Z, Pak JW, Lee D, McKiernan SH, McKenzie D, Weindruch R, Aiken JM. (2004). Molecular analyses of mtDNA deletion mutations in microdissected skeletal muscle fibers from aged rhesus monkeys. Aging Cell 3:319–26. Horai S, Satta Y, Hayasaka K, Kondo R, Inoue T, Ishida T, Hayashi S, Takahata N. (1992). Man’s place in Hominoidea revealed by mitochondrial DNA genealogy. J Mol Evol 35:32–43. Li D, Fan L, Zeng B, Yin H, Zou F, Wang H, Meng Y, et al. (2009). The complete mitochondrial genome of Macaca thibetana and a novel nuclear mitochondrial pseudogene. Gene 429:31–6. Richardson M, Mittermeier RA, Rylands AB, Konstant B. (2008). Macaca nemestrina. IUCN. The IUCN Red List of Threatened Species. Available at: www.iucnredlist.org (Accessed 12 February 2015). Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9. Wang J, Tang Y, Li S, Mai C, Gong Y. (2014). The complete mitochondrial genome of Japanese macaque, Macaca fuscata fuscata (Macaca, Cercopithecinae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.961137.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Southern pig-tailed macaque, Macaca nemestrina, and comparative mitochondrial genomics of Macaca species Chen Chen1, Huixian Mei2, and Xueting Luo1
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/30/15 For personal use only.
1
Clinical School of University of Hubei Chinese Medicine, Wuhan, Hubei, China and 2Physical Culture of Institute of Hubei University, Wuhan, Hubei, China Abstract
Keywords
In this study, we report the complete mitochondrial genome sequence of Southern pig-tailed, Macaca nemestrina for the first time. The genome is found to be 16,560 bp in length and has a base composition of A (32.25%), G (12.31%), C (30.51%), and T (24.93%), indicating that the percentage of A + T (57.18%) was higher than G + C (42.82%). Similar to other monkeys, it contains a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Most of the genes were located on the H-strand except for the ND6 gene and 8 tRNA genes. To obtain a more complete understanding of the evolutionary history of Macaca genus, 11 mitochondrial genomes were used for phylogenetic analysis. This mitochondrial sequence reported here would be useful to uncover the monkey’s evolution and add a new genetic resource for the genus Macaca.
Macaca nemestrina, mitochondrial genome, phylogenetic analysis
The Southern pig-tailed macaque, Macaca nemestrina, is a medium-sized primate with light brown fur, which is found in a portion of Southeast Asia from southern Thailand to the island of Borneo (Richardson et al., 2008). It is a species of genus Macaca. To date, more than 20 different species were recognized in the genus of Macaca (Fooden, 1976). Here, using the CLC Genomic Workbench v3.6 (2010), we assembled and analyzed the mitochondrial genome of Southern pig-tailed macaque, Macaca nemestrina. The blood sample was obtained from an individual and total genomic DNA was extracted and sequenced. We downloaded the genome raw reads, which were sequenced by Illumina HiSeq 2000, from NCBI (http://www.ncbi.nlm.nih.gov/ sra/). This mitochondrial sequence reported here would be useful to uncover the monkey’s evolution and add a new genetic resource for the genus Macaca. The complete mitogenome of M. nemestrina was 16,560 bp in length (GenBank accession No. KP765688). It harbored a total of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12 S rRNA and 16 S rRNA) and 1 non-coding control region (D-loop). Most of these genes were located on the H-strand except for the ND6 subunit gene and 8 tRNA genes, which were encoded on the L-strand. The arrangement of all genes did not differ significantly in comparison with other monkeys (Horai et al., 1992; Li et al., 2009; Wang et al., 2014). The overall base composition was 32.25% of A, 24.93% of T, 30.51% of C, and 12.31% of G, so the percentage of A and T (57.18%) was slightly higher than that of G and C (42.82%).
History Received 12 February 2015 Accepted 28 February 2015 Published online 22 May 2015
The total length of the 13 identified protein-coding genes was 11,355 bp, and they encoded 3791 amino acids in all. The 22 tRNA genes of M. nemestrina, ranging from 59 bp (tRNA-Ser) to 75 bp (tRNA-Leu), were determined based on their respective anticodons and secondary structures. The control region (CR) or D-loop region of the Southern pig-tailed macaque is located between tRNA-Pro and tRNA-Phe, and is 1082 bp. The total length of 12 S rRNA gene and 16 S rRNA gene is 948 bp and 1561 bp, respectively. To obtain a more complete understanding of the evolutionary history of Macaca genus, 11 mitochondrial genomes were used for phylogenetic analysis. Multiple alignments of these fragments were performed using MUSCLE (Edgar, 2004) with the default settings. The complete mitochondrial genome sequences of 10 other Macaca species are available from GenBank and the names of these species are as follows: M. arctoides, M. assamensis, M. fascicularis, M. fuscata, M. mulatta, M. silenus, M. sylvanus, M. thibetana, M. nigra, M. tonkeana (Arnason et al., 2001; Gokey et al., 2004; Li et al., 2009; Wang et al., 2014). The phylogenetic tree from maximum-likelihood (ML) was reconstructed using the MEGA5 (Tamura et al., 2011). Our analysis revealed three major clades within the Macaca (Figure 1), and one clade consists of M. nemestrina and three macaques. In this clade M. mulatta and M. fuscata formed a sister group to M. nigra, then grouped with M. nemestrina, which suggests that M. nemestrina emerged earlier than M. mulatta and M. fuscata. The other two clades consist of 4 species and 3 species, respectively.
Correspondence: Xueting Luo, Clinical School of University of Hubei Chinese Medicine, Wuhan, Hubei, China. Tel/Fax: +86-027-68889091. E-mail: [email protected]
2
C. Chen et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/30/15 For personal use only.
Figure 1. Phylogeny based on mtDNA sequences. The maximum-likelihood tree is drawn to scale. Mt genome size and AT content shown for each species. The NCBI accession number corresponds to each sequence.
Acknowledgements We would like to thank anonymous reviewers for providing valuable comments on the manuscript.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Arnason U, Gullberg A, Burguete AS, Janice A. (2001). Molecular estimates of primate divergences and new hypotheses for primate dispersal and the origin of modern humans. Hereditas 133:217–28. CLC Genomics Workbench v3.6. (2010). Available at: http:// www.clcbio.com/products/clc-genomics-workbench/ (Accessed 11 March 2015). Edgar RC. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–7. Fooden J. (1976). Provisional classification and key to living species of macaques (Primates: Macaca). Folia Primatol 25:225–36.
Gokey NG, Cao Z, Pak JW, Lee D, McKiernan SH, McKenzie D, Weindruch R, Aiken JM. (2004). Molecular analyses of mtDNA deletion mutations in microdissected skeletal muscle fibers from aged rhesus monkeys. Aging Cell 3:319–26. Horai S, Satta Y, Hayasaka K, Kondo R, Inoue T, Ishida T, Hayashi S, Takahata N. (1992). Man’s place in Hominoidea revealed by mitochondrial DNA genealogy. J Mol Evol 35:32–43. Li D, Fan L, Zeng B, Yin H, Zou F, Wang H, Meng Y, et al. (2009). The complete mitochondrial genome of Macaca thibetana and a novel nuclear mitochondrial pseudogene. Gene 429:31–6. Richardson M, Mittermeier RA, Rylands AB, Konstant B. (2008). Macaca nemestrina. IUCN. The IUCN Red List of Threatened Species. Available at: www.iucnredlist.org (Accessed 12 February 2015). Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9. Wang J, Tang Y, Li S, Mai C, Gong Y. (2014). The complete mitochondrial genome of Japanese macaque, Macaca fuscata fuscata (Macaca, Cercopithecinae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.961137.
