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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.

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