ABSTRACT
Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.
ABSTRACT
RNA was extracted from spleens of diarrhea and non-diarrhea piglets of Jiuyang Pig, Jianbai Pig and Landrace. RNA pools were established and DDRT-PCR using three anchored and seven arbitrary primers combined with silver staining was conducted to identify ESTs differentially expressed in diarrhea resistance to E. coli K88. Five cDNA were identified in the non-diarrhea RNA pools. Among them two are new sequences and three are highly identical to the ESTs in the GeneBank, of which two have known functions. One is the mammalian Nck adaptor protein 1 and the other is the human LINE-1 reverse transcriptase.