摘要A reference genome assembled from a single individual cannot capture the complex population level of polymorphism,especially for genetically divergent or admixed populations(Sherman et al.,2019).A complete genome data representative of a species rather than one individual,termed as pan-genome,can recover the genomic diversity and variations that are absent in the reference genome.Notably,using the assemblies of closely related species could efficiently recover the missing sequences and improve the mappability of the reference genome,which was confirmed in goat pan-genome(Li et al.,2019a).The gene pool of cattle(mainly contrib-uted by taurine and indicine cattle),representing one of the most important livestock in the world,is more complexed,with genetically and geographically diverse populations and origins(Verdugo et al.,2019).In addition,the mapping ability of the sequencing data of DNA samples to the reference genome can vary greatly because of incomplete lineage sorting(ILS)and pervasive intra-and inter-species introgression that further increase the complex of genetic variation in cattle,as well as the genus Bos(Chen et al.,2018;Wu et al.,2018).