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Nuclear mitochondrial DNA (nmtDNA) from diverse animals has been used to investigate mitochondrial phylogeny, including the use of pig as a surrogate for monkey nmtDNA. This surrogate system is problematic, however, as (1) pig nmtDNA is structurally homologous to that of primates and (2) monkey mitochondria are generally more divergent than those of other mammals. Here, we investigated the applicability of the pig nmtDNA surrogate to the primate cytoplasmic DNA (cDNA) by amplifying and sequencing a region of the mitochondrial genome from cynomolgus monkey (Macaca fascicularis) cells and tissues. Sequencing the macaque mitochondrial genome revealed that it exhibits a mosaic organization of mtDNA molecules, which has been reported for other hominoids. Cynomolgus monkey sequences were found in 49 of 60 selected tissues and contain multiple mtDNA genotypes that correspond to haplogroups found in the natural distribution of the macaque species. The majority of the mtDNAs were found in liver and kidney and contained a substantial number of mitochondrial genomes belonging to the N sub-haplogroup that is not found in human cells. The results revealed that the cDNA/mtDNA polymorphisms of the cynomolgus monkey cannot be used as a substitute for human cDNA/mtDNA in molecular analysis of mitochondrial phylogeny. This study also demonstrates that the use of the pig mtDNA homologue as a surrogate for macaque nmtDNA would be a useful tool to study mitochondrial systems with low sequence conservation.Q:
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