Isolation and characterization of DNA barcodes from distinctive and rare terrestrial animals in China using universal COI and 16S primers

Mali Guo; Zhenzhen Peng; Xiaoting Zhang; Chaohai Yuan; Hanxi Lu; Keyuan Zhang; Yafei Cai; Wei Zhang

doi:10.37175/stemedicine.v2i7.95

Mali Guo College of Animal Science and Technology Nanjing Agricultural University 210095 Nanjing, China; National Experimental Teaching Demonstration Center of Animal Science Nanjing Agricultural University 210095 Nanjing, China
Zhenzhen Peng College of Animal Science and Technology Nanjing Agricultural University 210095 Nanjing, China; National Experimental Teaching Demonstration Center of Animal Science Nanjing Agricultural University 210095 Nanjing, China
Xiaoting Zhang College of Animal Science and Technology Nanjing Agricultural University 210095 Nanjing, China; National Experimental Teaching Demonstration Center of Animal Science Nanjing Agricultural University 210095 Nanjing, China
Chaohai Yuan College of Animal Science and Technology Nanjing Agricultural University 210095 Nanjing, China; National Experimental Teaching Demonstration Center of Animal Science Nanjing Agricultural University 210095 Nanjing, China
Hanxi Lu College of Animal Science and Technology Nanjing Agricultural University 210095 Nanjing, China; National Experimental Teaching Demonstration Center of Animal Science Nanjing Agricultural University 210095 Nanjing, China
Keyuan Zhang College of Life Science Nanjing Agricultural University 210095 Nanjing, China
Yafei Cai College of Animal Science and Technology Nanjing Agricultural University 210095 Nanjing, China; National Experimental Teaching Demonstration Center of Animal Science Nanjing Agricultural University 210095 Nanjing, China
Wei Zhang College of Animal Science and Technology Nanjing Agricultural University 210095 Nanjing, China; National Experimental Teaching Demonstration Center of Animal Science Nanjing Agricultural University 210095 Nanjing, China

DOI: https://doi.org/10.37175/stemedicine.v2i7.95

Keywords: DNA barcode, COI, 16S, indigenous animals, China

Abstract

Background: Accurate taxonomic identification is the cornerstone for monitoring, conservation and management of ecological resources. China has the highest biodiversities and the richest species assemblages in the world, but is lacking in sufficient assessment to the abundant genetic variability. DNA barcoding is a proven tool employing sequence information for rapid and unambiguous species delineation. However, the ability of barcodes to distinguish species that are archaic and distinctive evolutionary lines remains largely untested.
Methods: In order to investigate the resources of terrestrial animals in China, regions from mitochondrial COI and 16S are barcoded for 395 specimens belonging to 54 selected species, many of which are indigenous representatives in danger. High success rate of PCR amplification is achieved by using universal COI and 16S primers with many numts pseudogenes co-amplified from mammalian samples.
Results: Application of barcodes to flag species is generally straightforward since no COI or 16S haplotypes are shared between closely related species. Barcoding gap, species resolution and phylogenetic relationships relying on our barcode libraries are further compared using distance and tree based approaches.
Conclusion: Results show that the discriminatory power of the two barcode markers could differentiate on a case-by-case basis, and also suggest a careful consideration of the nuclear numts for barcoding studies as they might provide a new understanding for evolution.

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