Development of short-target primers for species identification in biological studies of Carnivora

Huiwen Liu; Dan Wang; Chenglin Zhang; Tianchun Pu; Lijuan Xiong; Fuwen Wei; Yibo Hu

doi:10.1002/ece3.10135

Development of short-target primers for species identification in biological studies of Carnivora

Ecol Evol. 2023 May 25;13(5):e10135. doi: 10.1002/ece3.10135. eCollection 2023 May.

Authors

Huiwen Liu^{1

2}, Dan Wang^{1

2}, Chenglin Zhang³, Tianchun Pu³, Lijuan Xiong⁴, Fuwen Wei^{1

2}, Yibo Hu^{1

2}

Affiliations

¹ CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology, Chinese Academy of Sciences Beijing China.
² University of Chinese Academy of Sciences Beijing China.
³ Beijing Zoo Beijing China.
⁴ School of Life Sciences Guizhou Normal University Guiyang China.

Abstract

Noninvasive genetic sampling greatly facilitates studies on the genetics, ecology, and conservation of threatened species. Species identification is often a prerequisite for noninvasive sampling-based biological studies. Due to the low quantity and quality of genomic DNA from noninvasive samples, high-performance short-target PCR primers are necessary for DNA barcoding applications. The order Carnivora is characterized by an elusive habit and threatened status. In this study, we developed three pairs of short-target primers for identifying Carnivora species. The COI279 primer pair was suitable for samples with better DNA quality. The COI157a and COI157b primer pairs performed well for noninvasive samples and reduced the interference of nuclear mitochondrial pseudogenes (numts). COI157a could effectively identify samples from Felidae, Canidae, Viverridae, and Hyaenidae, while COI157b could be applied to samples from Ursidae, Ailuridae, Mustelidae, Procyonidae, and Herpestidae. These short-target primers will facilitate noninvasive biological studies and efforts to conserve Carnivora species.

Keywords: COI; Carnivora; noninvasive sample; species identification.