Efficiency of the mitochondrial DNA markers (COI, cyt b) and a nuclear DNA marker (RAGI) in molecular identification of zoonotic diseases' hosts

Morphological and allozyme studies are not remarkably efficient in identification of cryptic and unknown species; therefore, the differences between intra-and interspecific genetic variation (DNA barcoding) have been applied in recent decades. Applying molecular markers has been common for identification of taxa, so that suitable marker choice representing high divergence is a crucial issue to reveal taxonomic status of the taxa in this approach.
In this analytical study, the performance of two mitochondrial markers including cytochrome c oxidase subunit I (COI) and cytochrome b (cyt b)was compared with nuclear recombination activating protein I locus(RAGI), and their efficiency in identification of mammal taxa as the host of zoonotic diseases was evaluated. The COI, cyt b, and RAGI sequences were retrieved from GenBank. Intra-and interspecific genetic distances were estimated and compared at the species level. The variances in genetic divergence were also calculated and compared between the markers.
  Our results showed a wide gap between intra-and interspecific genetic distances for both COI and cyt b markers and less apparent gap for RAGI, indicating that this nuclear marker is less proper for species delimitation in DNA barcoding.
We concluded that in the case of multiple sequences available COI, contributes to accurate differentiation at the species level, showing a significant gap between intra-and interspecific genetic distances and may play an important role as DNA barcoding marker.