The availability of reference genomes has been the foundation for genomics research in the last decade.However, as reports of presence/absence variations of sequence and genes are growing in various species (Zhang et al., 2016;Sun et al.,2018), it is increasingly evident that a single reference genome provides an inadequate representation of the whole landscape of sequence diversity within a species.Pan-genome analysis provides a platform to investigate the entire genome repertoire of a biological clade.In plant species, a recent wave of pangenome studies has uncovered extensive gene content variations and linked them with major agronomical traits andadaptation (Zhao et al., 2018;Tao et al., 2019b;Gao et al., 2019).However, most of the pan-genomes reported todate using de novo assembly strategies arebased on fragmented genome assemblies, which has limited their capacity to provide an accurate guide for genomics research.Thanks to the continuing advances in sequencing technology, a soybean pan-genome based on 29 reference-quality assemblies was recently constructed by Tian and colleagues (Liu et al., 2020), which could replace the currently available reference genome based on a cultivated line (Schmutz et al., 2010) to become the new guide for soybean genomics research.