A high-quality chromosome-level genome assembly and annotation of Anqing Six-end-white pig (Sus scrofa)

The Anqing Six-end-white pig, a precious Chinese autochthonous breed, is mainly distributed in the Anhui Province, China. It is well documented for its excellent meat quality and crude-feed tolerance. However, the current lack of high-quality Anqing Six-end-white pig genome assembly poses a significant limitation for elucidating its germplasm characteristics and implementing genomic-level conservation. In this study, we assembled a high-quality chromosome-level genome; the genome size was 2.66 Gb with contig N50 = 90.48 Mb and scaffold N50 = 143.10 Mb. There were 23 gaps in the final assembled genome. A total of 1.16 Gb repeat sequences were identified and accounting for 43.52% of the genome. A total of 20,809 protein-coding genes were identified, and 99.18% of these genes were annotated. The predicted non-coding genes included 848 miRNAs, 4544 tRNA, 253 rRNA, and 2156 snRNAs in the genome. Genome completeness was 98.67% using BUSCO and 99.81% using Compleasm. This chromosome-level assembly provides a robust scientific foundation for the conservation, breeding, and exploration of genetic traits in the Anqing Six-end-white pig.