Abstract
A high-quality reference genome coupled with resequencing data is a promising strategy to address issues in conservation genomics. This has greatly enhanced the development of conservation plans for endangered species. Pangolins are fascinating animals with a variety of unique features. Unfortunately, they are the most trafficked wild animal in the world. In this study, we assembled a chromosome-scale genome with HiFi long reads and Hi-C short reads for the Chinese and Malayan pangolin and provided two new representative reference genomes for the pangolin species. We found a great improvement in the evaluation of genetic diversity and inbreeding based on these high-quality genomes and obtained different results for the detection of genome-wide extinction risks compared with genomes assembled using short reads. Moderate inbreeding and genetic diversity were reverified in these two pangolin species, except for one Malayan pangolin population with high inbreeding and low genetic diversity. Moreover, we identified a much higher inbreeding level (FROH = 0.54) in the Chinese pangolin individual from Taiwan Province compared with that from Mainland China, but more than 99.6% runs of homozygosity (ROH) fragments were restricted to less than 1 Mb, indicating that the high FROH in Taiwan Chinese pangolins may have accumulated from historical inbreeding events. Furthermore, our study is the first to detect relatively mild genetic purging in pangolin populations. These two high-quality reference genomes will provide valuable genetic resources for future studies and contribute to the protection and conservation of pangolins.