Chromosome-level genome assembly of the Shanghai Pudong White Pig (Sus scrofa domesticus)

Abstract The Pudong White Pig (PD) is the only indigenous pig breed in China with entirely white-colored coat and is listed as endangered livestock breed. This study conducted a de novo whole-genome assembly of the PD using PacBio third-generation sequencing combined with Hi-C technology. Following the de-redundancy step, the statistics of the PD assembly showed that the total sequence length is approximately 2.68 Gb. The PD genome assembly obtained in this study exhibits higher sequence integrity and fewer genomic gaps compared to the currently most widely used Duroc pig reference genome Sscrofa11.1. The pan-genome was constructed from 30 domestic and international pig breeds, and identified a total of 135,859 non-reference sequences (NRSs). After quality control filtering, 65,193 NRSs were validated, with a combined length of 108.33 Mb. A total of 594 Shanghai indigenous pig breeds-specific NRSs were identified across the four Shanghai indigenous pig populations. For instance, the NRSs insertion site specific to the BMPR1B gene, which is linked to reproductive performance in Taihu lake pigs in China. Additionally, the study revealed a hotspot region for NRSs at the center (59–89 Mb) region of the chromosome X. Finally, this study also confirmed a previously reported splice mutation at Chr 8: 41,486,012 of Sscrofa11.1 pig reference genome. At this locus, both the PD and Shanghai White breed (SHW) exhibit the same dominant white genotype characteristics as the Landrace and Yorkshire breed. The study has assembled the first high-quality reference genome for the PD pig, providing new insights into the genomic characterization and phenotypic analysis of Chinese indigenous pig breeds.