Supporting data for "Enhancing inbreeding estimation and global conservation insights through HiFi assemblies of Chinese and Malayan pangolin"

A high-quality reference genome coupled with resequencing data is becoming a promising strategy to address issues in conservation genomics, which has greatly enhanced the development of conservation plans for endangered species. Pangolins are fascinating animals with a range of distinctive features, but unfortunately, they are the world's most trafficked wild animals. Here, we report a haplotype-resolved and chromosome-scale genome for each of the Chinese pangolin and Malayan pangolin, the most representative reference genome for pangolin species. We found a greater improvement in evaluation of genetic diversity and inbreeding based on high-quality genomes and obtained different results in detecting genome-wide extinction risks being compared with short read assembled genomes. Moderate inbreeding and genetic diversity were verified again in these two pangolin species except for one Malayan pangolin population with the high inbreeding and low genetic diversity, which we recommend to pay special attention to the conservation and protection of this population. Additionally, our study is the first to detect relative mild genetic purging in pangolin populations that were analyzed. These two high quality reference genomes will provide valuable genomic resource for future studies on the protection and conservation for pangolins.