South American camelids comprise the guanaco (Lama guanicoe) and the vicuña (Vicugna vicugna), which are wild species, and the domestic llama (Lama glama) and alpaca (Lama pacos). This paper presents the first complete mitochondrial (mt) genome of the guanaco and the mt coding sequence of the vicuña. The guanaco mtDNA is 16,649 nt long and its composition and organization are similar to the mitochondrial genome of other mammals. Excluding the control region, comparison of the complete guanaco and vicuña mtDNA showed 4.4% sequence divergence. Nucleotide differences in peptide coding genes varied from 1.9% in ATP6 to 6.4% in Cyt b. These values are compatible with the close relatedness of both species identified by other authors. Based on the differences between the control region sequence here reported and that previously described, we also discuss the occurrence of NUMTs in the genome of South American camelids.
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