title: Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy.
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.
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Yu-Feng
authors.initials: YF
authors.lastname: Huang
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Mohit
authors.initials: M
authors.lastname: Midha
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Tzu-Han
authors.initials: TH
authors.lastname: Chen
authors.affiliation: National Center for High-Performance Computing, Hsinchu, Taiwan.
authors.forename: Yu-Tai
authors.initials: YT
authors.lastname: Wang
authors.affiliation: Department of Anthropology, University of California Davis, Davis, CA, United States of America.
authors.forename: David Glenn
authors.initials: DG
authors.lastname: Smith
authors.affiliation: Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan.
authors.forename: Kurtis Jai-Chyi
authors.initials: KJ
authors.lastname: Pei
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan; College of Life Science, National Taiwan University, Taipei, Taiwan; Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.
authors.forename: Kuo Ping
authors.initials: KP
authors.lastname: Chiu
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D014644:Genetic Variation / Q000235:genetics; D054629:Genome, Mitochondrial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008251:Macaca / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods; D013624:Taiwan