Fig. 1: Phylogeny of bovine species and pan-genome of wild and domestic yaks.

a Phylogenetic tree of 47 bovine individuals with de novo genomes-based SNPs with buffalo as outgroup. CDMC Chaidamu cattle, TC Tibetan cattle, ZMC Zhangmu cattle, WNC Wannan cattle, BS Brown Swiss, OBV Original Braunvieh, SA Sanga Ankole, ARS-UCD1.2, Btau_5.0.1 and UMD_3.1.1: Hereford cattle. b A cladogram of Bovini species based on single-copy genes in the individuals marked with a red star in Fig. 1a. c Variation of gene families in the pan-genome and core genome along with an additional yak genome. d Numbers and frequencies of core, near-core, and variable gene families. e, f The gene expression levels and Ka/Ks values of core (16,900; 12,532), near-core (4186; 2875), and variable genes (2934; 774) of yaks. Lowercase letters indicate significant differences (p < 0.05); two-sided Student’s t-test. Box edges indicate the upper and lower quartiles, the centerlines indicate the median value, the horizontal bars indicate the maximum and minimum values, and the dots indicate outliers. g numbers of genes without homologues in the wild assemblies (“new genes”) and genes originating from cattle as inferred from their phylogenetic position (“introgression genes”). h Heat map representing the number of genes present in the assembly on the X-axis but not in the assembly on the Y-axis.