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About Glycine max (soybean)
Soybean is a crop legume that globally constitutes one of the most important sources of animal feed protein and cooking oil. Having originated in East Asia soy is now cultivated world-wide with greatest production in the U.S. Though only a minor proportion of the crop is eaten directly by humans, soybean is a valuable source of protein, containing all essential amino acids, and frequently used as a dietary substitute for meat. Like other legumes, soybean is able to fix atmospheric nitrogen by engaging in a symbiotic relationship with microbial organisms. The complete sequence of the soybean genome not only impacts research and breeding of this crop, but also serves as a reference for genomics research in other legumes. Representing the order Fabales within the eudicot taxonomy, the sequence will also advance research in comparative phylogenomics. As a paleopolyploid, the soybean genome shows evidence of two ancient whole genome duplications, one early in the legume lineage and a second more recent event specific to the soybean lineage [1]. The soybean genome has 20 chromosomes and an estimated size of 1,115 Mb.
Genome Sequencing and Gene Prediction (release Glyma1.0)
Glycine max var. Williams 82 was sequenced, assembled, and annotated by the U.S. Department of Energy Joint Genome Institute (JGI) in collaboration with a consortium of research labs and published in 2010 [1]. About 13 million shotgun Sanger reads were assembled into 20 chromosomes totaling 975 Mb with an additional amount in unmapped scaffolds. Genes were annotated with the aid of ~1.6 M ESTs and by ab initio prediction. A total of 66,153 protein-coding loci were predicted and classified into six levels of support (see JGI Phytozome for additional details).
Gramene/Ensembl Genomes Annotation
Additional annotations generated by the Gramene/Ensembl Genomes projects include:
- The standard set of Gramene analyses are detailed here.
- Phylogenetic gene trees and whole-genome alignments with several plant and metazoan species, using the Ensembl Compara pipeline
Links
Citations
- Schmutz J, et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature. 463(7278):178-83. Erratum in: Nature. 2010 May 6;465(7294):120. PMID: 20075913
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