Genome sequence of the palaeopolyploid soybean

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. Soybean (Glycine max) is an important commercial crop providing both protein and oil, and its symbiotic relationship to nitrogen-fixing bacteria makes it a profitable crop in rotation systems. Its genome has now been sequenced: it is the first legume and at 1.1 gigabases, the largest plant genome to be sequenced by whole-genome shotgun techniques. Soybean has a colourful genetic past; genome duplications occurred at 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. An accurate soybean genome sequence should accelerate the creation of improved soybean varieties. Soybean is an important crop plant, providing seed protein and oil and fixing atmospheric nitrogen through symbioses with soil-borne microorganisms. Using a whole-genome shotgun approach, its 1.1-gigabase genome is now sequenced and integrated with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly.