The pan-genome of the cultivated soybean (PanSoy) reveals an extraordinarily conserved gene content

Studies on structural variation in plants have revealed the inadequacy of a single reference genome for an entire species and suggest that it is necessary to build a species-representative genome called a pan-genome to better capture the extent of both structural and nucleotide variation. Here, we present a pan-genome of cultivated soybean (Glycine max), termed PanSoy, constructed using the de novo genome assembly of 204 phylogenetically and geographically representative improved accessions selected from the larger GmHapMap collection. PanSoy uncovers 108 Mb (similar to 11%) of novel nonreference sequences encompassing 3621 protein-coding genes (including 1659 novel genes) absent from the soybean 'Williams 82' reference genome. Nonetheless, the core genome represents an exceptionally large proportion of the genome, with >90.6% of genes being shared by >99% of the accessions. A majority of PAVs encompassing genes could be confirmed with long-read sequencing on a subset of accessions. The PanSoy is a major step towards capturing the extent of genetic variation in cultivated soybean and provides a resource for soybean genomics research and breeding.

Automated summary

The construction of a pan-genome for cultivated soybean reveals a significant amount of novel genes, with over 90.6% of genes in the core genome shared by 99% of accessions. The PanSoy represents a major advancement in capturing the extent of genetic variation in cultivated soybean, serving as a valuable resource for soybean genomics research and breeding.