Genome sequence of the palaeopolyploid soybean

TLDR

Soybean (Glycine max) is a major crop valued for its seed protein, oil, and nitrogen‑fixing symbiosis with soil microorganisms. An accurate soybean genome sequence will enable identification of the genetic basis of many traits and accelerate breeding of improved varieties. The authors sequenced the 1.1‑gigabase genome by whole‑genome shotgun and integrated it with physical and high‑density genetic maps to produce a chromosome‑scale draft assembly. The draft predicts 46,430 protein‑coding genes—70 % more than Arabidopsis and comparable to poplar—most of which (≈78 %) cluster at chromosome ends, and reveals two ancient polyploidy events (≈59 Myr and 13 Myr ago) that produced a highly duplicated genome with ~75 % of genes in multiple copies, followed by gene diversification, loss, and extensive chromosome rearrangements.

Abstract

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.