Summer Diet of South China Sika Deer (Cervus nippon kopschi) in Taohongling based on High-Throughput Sequencing and Metabarcoding trnL

ABSTRACT The sika deer (Cervus nippon) is listed as a Class I National Key protected wild animal and is an endemic species in the East Asian monsoon region. Although the species as a whole is thriving, it is endangered and locally extinct in many areas of China, and the South China sika deer (Cervus nippon kopschi) is one of three subspecies left in China. Diet analysis is one of the core contents in studying animal habitat requirements, and a study of their diet could provide valuable reference for species conservation and management. The metabarcoding trnL regions of the chloroplast genome from 30 fecal samples of Taohongling sika deer were amplified with universal primers and sequenced by high-throughput. We found that 28 out of 30 valid samples had a total of 677,856 valid amplified sequences with an average valid sequence of 24,209.14±323.83. A total of 326 OTUs were obtained from 28 valid samples, and the MP, SS, and NJS groups shared 222 OTUs, accounting for 68.09% of the total OTUs. OTUs alignment indicated that the forage plants of sika deer belong to 82 families, and 110 genera. An alpha diversity analysis showed that there was no significant difference (p > 0.05). The NMDS analysis found considerable overlap at the three sampling sites, and the niche breadths of SS (Fir forests), MP (The nursery base), and NJS (Nie Jiashan) were 9.593, 9.426, and 9.419, respectively. High-throughput sequencing and metabarcoding trnL could provide higher taxonomic resolution, identify more food items, and can simultaneously analyze a larger number of samples compared with traditional diet methods. This study assembled basic summer diet data and provided an important accumulation for the protection and monitoring of Taohongling sika deers, which also provides reference for the establishment of local database in the future.