Fig. 1: Goat T2T genome assembly with 29 autosomes and chromosomes X and Y.

a Genome assembly strategy for T2T-goat1.0 and its haplotype genomes T2T-goat1.0P and T2T-goat1.0M of a buck. Trio-binning assemblies for the autosomes of T2T-goat1.0P and T2T-goat1.0M and Y chromosome were performed based on long reads of the buck and MGI short reads from its parents. b The assembly graph string shows a tangle among the four chromosomes, Chr12, Chr13, Chr19 and Chr22, due to the high similarities of centromeric sequences in gray. The centromeric regions in the assembly tangle are enlarged and shown in the right panel. c, d Genome features of Chr12 and Chr19 in T2T-goat1.0. The assembly graph tangle involving Chr12, Chr13, Chr19 and Chr22 was resolved in T2T-goat1.0, and Chr12 and Chr19 are selected to exhibit the completeness and features across the whole chromosome. The following information is provided from top to bottom: the gene density (red), the density of LINEs and SINEs (orange), the satellite density (green), the TE density (blue), error k-mer (k = 21, purple), and the minimum unique k-mer (MUK) per 100 kb. The more MUK values indicate more repetitive sequences in a 100-kb window, and more yellow and green colors indicate the presence of the centromeric regions. All the features are shown in 10-kb windows, except for MUK.