NRGene assembles two soybean genomes for protein & oil

Dr. Henry Nguyen, a Curators' distinguished professor of plant sciences in the University of Missouri College of Agriculture, Food & Natural Resources, has employed NRGene's DeNovoMAGIC, the world's most popular genome assembly tool for crop plants, to assemble two genomes of soybean: "Lee," a Glycine max variety, and a Glycine soja accession PI 483463. The Lee variety constitutes an important parent in U.S. southern breeding lines, while the G. soja accession is a wild soy line, very different from the cultivated varieties.

Soybeans are increasingly relied upon as a source of oil and protein across the globe, both for animal and human use. With the knowledge delivered by the increasing number of comprehensive genome assemblies, scientists can use traditional breeding to increase simultaneously the oil and protein volume and nutritional value produced within a single plant.

350 million metric tons of soybeans are grown around the world. United States grows 35% of the world's soybeans, with Brazil a close second at 29% and Argentina at 18%. The soybean grain market itself is worth more than $40 billion in the United States alone. (FAOSTAT 2016)

"United Soybean Board is pleased to have contributed to this important set of data. These investments in technology will directly help breeders to improve soybean lines for sustainability and traits like improved oils and meal components," said Jackie Weiss, USB Director of Digital Agriculture, Bioinformatics and Molecular Biology.

In addition to the United Soybean Board, funding for the sequencing project was provided by three private companies: Bayer CropScience, DOW AgroSciences and Monsanto.

NRGene's DenovoMAGIC 2.0 was used to deliver the Lee and G. soja assemblies, resulting in genome assembly sizes of 1,021 MB and 960 MB and N50 scaffold sizes of 4.57 MB and 4.44 MB with BUSCO scores of 94.9% and 95.3% respectively. Those are the most accurate and complete genome representations of these cultivars.

DeNovoMAGIC can assemble virtually any genome de novo from Illumina short reads, completing even the most challenging assemblies within days to weeks of obtaining the raw sequence data. The latest version, DeNovoMAGIC 3.0, produces long, accurate, and phased scaffolds from NGS data even for large, highly repetitive, polyploid, and heterozygous genomes.

The soybean team, in addition to NRGene, included a group of scientists from the University of Missouri, the U.S. Department of Agriculture's Agricultural Research Service (ARS), the HudsonAlpha Institute for Biotechnology, Pacific Biosciences, Bionano Genomics and Washington University, in addition to international collaborations with the University of Western Australia and the Chinese University of Hong Kong. These researchers utilized a variety of data for quality control and to add to the already high quality NRGene assemblies. Recently, both genome sequences were released to the soybean database - www.soybase.org

"We must secure highly nutritional food for the ever-growing world population, and the soybean is a key resource for global oil and protein consumption," said Dr. Gil Ronen, NRGene's CEO. "Soy researchers can now plumb the depths of the genome more easily in order to discover the critical traits necessary to create hardier species with higher nutritional values."