Glycine max Assembly and Gene Annotation

About Glycine max

Glycine max (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. The soybean genome has 20 chromosomes and an estimated size of 1,115 Mbp.

Assembly

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. About 13 million shotgun Sanger reads were assembled into 20 chromosomes totalling 975 Mbp with an additional amount in unmapped scaffolds.

Annotation

The v1.1 gene set integrates ~1.6 M ESTs and 1.5 billion paired-end Illumina RNA-seq reads with homology- and ab initio-based gene predictions. A total of 54,175 protein-coding loci were predicted and classified into six levels of support (see JGI Phytozome for additional details).

Links

References

  1. Genome sequence of the palaeopolyploid soybean.
    Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J et al. 2010. Nature. 463:178-183.
  2. Image credit: USDA.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyV1.0, INSDC Assembly GCA_000004515.1, Jan 2010
Database version90.1
Base Pairs973,344,380
Golden Path Length973,344,380
Genebuild byJGI
Genebuild methodImported from JGI-Phytozome
Data sourceJGI

Gene counts

Coding genes54,174
Non coding genes1,369
Small non coding genes1,354
Long non coding genes15
Gene transcripts74,688

Other

FGENESH gene prediction128,627

About this species