Extended Data Fig. 1: Assembly pipeline and quality control of the CPC samples.

a, Flowchart showing the steps and bioinformatic tools applied in quality control, assembly, and correction of 68 CPC samples used for the pan-genome construction. b, Quality control of the primary assemblies of 68 CPC samples, in which 3 samples (denoted by the red dots) with N50 <20 Mb or contig number ≥2000 were removed in subsequent analyses. c, Quality control of the diploid assemblies of 65 CPC samples, in which 14 haplotype assemblies (denoted by the red dots) of 7 samples with N50 <10 Mb or contig number ≥2000 were removed in subsequent analyses.