Fig. 1

Yak pangenome construction. A System diagram of Yak pangenome construction based on third- and second-generation sequencing data. This is an iterative alignment process. Initially, 16 yak individuals, each possessing both third-generation and second-generation sequencing data, were selected for de novo assembly. Following independent assembly, the generated sequences were aligned against the reference genome (BosGru3.0). The purpose of this process is indicated by the dashed box, which involves extracting nonreference sequences from the 16 genomes through homology-based alignments with the reference genome. This process is iterative, meaning that the nonreference sequences from the previous round are combined with the reference to form the ‘reference’ for the next round, thereby eliminating redundant sequences among the 16 genomes. Finally, all nonreference sequences were aligned against the reference genome again to further remove redundancy. B The fitted curve shows an increase in the total number of genes and a decrease in the number of core genes in the yak pangenome as individuals increase. Each given number of sample combinations was randomly selected 10,000 times. The upper and lower boundaries of the pink and green regions correspond to the maximum and minimum numbers of genes, respectively. C PCA based on binary gene PAV data. D Distribution of the number of core, softcore, shell and cloud genes. E Distribution of genes in Jinchuan, other domestic and wild yak populations. F Pfam enrichment analysis results of shell genes. G–H Shell genes were enriched (P < 0.05) in some GO terms belonging to cellular component and biological process