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Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy.

Huang YF, Midha M, Chen TH, Wang YT, Smith DG, Pei KJ, Chiu KP - PLoS ONE (2015)

Bottom Line: We compared the assembled mitogenome with that of other macaque species for phylogenetic analysis.Our results show that, the M. cyclopis mitogenome consists of 16,563 nucleotides encoding for 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs.The availability of the complete Taiwanese macaque mitogenome will facilitate the study of primate evolution and the characterization of genetic variations for the potential usage of this species as a non-human primate model for medical research.

View Article: PubMed Central - PubMed

Affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan.

ABSTRACT
The Taiwanese (Formosan) macaque (Macaca cyclopis) is the only nonhuman primate endemic to Taiwan. This primate species is valuable for evolutionary studies and as subjects in medical research. However, only partial fragments of the mitochondrial genome (mitogenome) of this primate species have been sequenced, not mentioning its nuclear genome. We employed next-generation sequencing to generate 2 x 90 bp paired-end reads, followed by reference-assisted de novo assembly with multiple k-mer strategy to characterize the M. cyclopis mitogenome. We compared the assembled mitogenome with that of other macaque species for phylogenetic analysis. Our results show that, the M. cyclopis mitogenome consists of 16,563 nucleotides encoding for 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. Phylogenetic analysis indicates that M. cyclopis is most closely related to M. mulatta lasiota (Chinese rhesus macaque), supporting the notion of Asia-continental origin of M. cyclopis proposed in previous studies based on partial mitochondrial sequences. Our work presents a novel approach for assembling a mitogenome that utilizes the capabilities of de novo genome assembly with assistance of a reference genome. The availability of the complete Taiwanese macaque mitogenome will facilitate the study of primate evolution and the characterization of genetic variations for the potential usage of this species as a non-human primate model for medical research.

No MeSH data available.


Insertion in tRNA-Tyr of the WANCY tRNA-gene cluster.Multiple sequence alignment of the WANCY tRNA-gene cluster identified a 17 bp insertion at the 3’-end of tRNA-Tyr specific to M. sylvanus and a 24 bp insertion at the 3’-end of tRNA-Tyr specific to M. mulatta. The red box showed the overlap region between tRNA-Tyr and COX1. The blue line showed the 3’-end boundary of tRNA-Tyr while checking with tRNAscan-SE and MITOS.
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pone.0130673.g005: Insertion in tRNA-Tyr of the WANCY tRNA-gene cluster.Multiple sequence alignment of the WANCY tRNA-gene cluster identified a 17 bp insertion at the 3’-end of tRNA-Tyr specific to M. sylvanus and a 24 bp insertion at the 3’-end of tRNA-Tyr specific to M. mulatta. The red box showed the overlap region between tRNA-Tyr and COX1. The blue line showed the 3’-end boundary of tRNA-Tyr while checking with tRNAscan-SE and MITOS.

Mentions: Multiple sequence alignment for the region of tRNA-Phe and tRNA-Pro (excluding control region) of the macaques under study revealed variations in the following regions. 17 and 24 bp long different insertions after tRNA-Tyr in WANCY region in M. sylvanus and M. mulatta respectively (Fig 5). There is a 20 bp overlap region between tRNA-Tyr and COX1 identified in M. mulatta (JQ821843). The 3’-end boundary of tRNA-Tyr is the same among all macaques. In our analysis with tRNAscan-SE [48] and MITOS, we found these two insertions and concluded them as result of annotation conflict. In addition, pairwise comparison with the same species from different publications this observation was confirmed. For M. sylvanus, we compared barbary macaque of GenBank acc. NC_002764 with that of GenBank acc. KJ567054. For M. mulatta, we compared Indian rhesus macaque of GenBank JQ821843 with both of them of GenBank acc. KJ567053 and NC_005943 respectively.


Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy.

Huang YF, Midha M, Chen TH, Wang YT, Smith DG, Pei KJ, Chiu KP - PLoS ONE (2015)

Insertion in tRNA-Tyr of the WANCY tRNA-gene cluster.Multiple sequence alignment of the WANCY tRNA-gene cluster identified a 17 bp insertion at the 3’-end of tRNA-Tyr specific to M. sylvanus and a 24 bp insertion at the 3’-end of tRNA-Tyr specific to M. mulatta. The red box showed the overlap region between tRNA-Tyr and COX1. The blue line showed the 3’-end boundary of tRNA-Tyr while checking with tRNAscan-SE and MITOS.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4488429&req=5

pone.0130673.g005: Insertion in tRNA-Tyr of the WANCY tRNA-gene cluster.Multiple sequence alignment of the WANCY tRNA-gene cluster identified a 17 bp insertion at the 3’-end of tRNA-Tyr specific to M. sylvanus and a 24 bp insertion at the 3’-end of tRNA-Tyr specific to M. mulatta. The red box showed the overlap region between tRNA-Tyr and COX1. The blue line showed the 3’-end boundary of tRNA-Tyr while checking with tRNAscan-SE and MITOS.
Mentions: Multiple sequence alignment for the region of tRNA-Phe and tRNA-Pro (excluding control region) of the macaques under study revealed variations in the following regions. 17 and 24 bp long different insertions after tRNA-Tyr in WANCY region in M. sylvanus and M. mulatta respectively (Fig 5). There is a 20 bp overlap region between tRNA-Tyr and COX1 identified in M. mulatta (JQ821843). The 3’-end boundary of tRNA-Tyr is the same among all macaques. In our analysis with tRNAscan-SE [48] and MITOS, we found these two insertions and concluded them as result of annotation conflict. In addition, pairwise comparison with the same species from different publications this observation was confirmed. For M. sylvanus, we compared barbary macaque of GenBank acc. NC_002764 with that of GenBank acc. KJ567054. For M. mulatta, we compared Indian rhesus macaque of GenBank JQ821843 with both of them of GenBank acc. KJ567053 and NC_005943 respectively.

Bottom Line: We compared the assembled mitogenome with that of other macaque species for phylogenetic analysis.Our results show that, the M. cyclopis mitogenome consists of 16,563 nucleotides encoding for 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs.The availability of the complete Taiwanese macaque mitogenome will facilitate the study of primate evolution and the characterization of genetic variations for the potential usage of this species as a non-human primate model for medical research.

View Article: PubMed Central - PubMed

Affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan.

ABSTRACT
The Taiwanese (Formosan) macaque (Macaca cyclopis) is the only nonhuman primate endemic to Taiwan. This primate species is valuable for evolutionary studies and as subjects in medical research. However, only partial fragments of the mitochondrial genome (mitogenome) of this primate species have been sequenced, not mentioning its nuclear genome. We employed next-generation sequencing to generate 2 x 90 bp paired-end reads, followed by reference-assisted de novo assembly with multiple k-mer strategy to characterize the M. cyclopis mitogenome. We compared the assembled mitogenome with that of other macaque species for phylogenetic analysis. Our results show that, the M. cyclopis mitogenome consists of 16,563 nucleotides encoding for 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. Phylogenetic analysis indicates that M. cyclopis is most closely related to M. mulatta lasiota (Chinese rhesus macaque), supporting the notion of Asia-continental origin of M. cyclopis proposed in previous studies based on partial mitochondrial sequences. Our work presents a novel approach for assembling a mitogenome that utilizes the capabilities of de novo genome assembly with assistance of a reference genome. The availability of the complete Taiwanese macaque mitogenome will facilitate the study of primate evolution and the characterization of genetic variations for the potential usage of this species as a non-human primate model for medical research.

No MeSH data available.