Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 7, 2009
Publication Date: February 17, 2010
Citation: Du, J., Grant, D.M., Tian, Z., Nelson, R., Zhu, L., Shoemaker, R.C., Ma, J. 2010. SoyTEdb: A Comprehensive Database of Transposable Elements in the Soybean Genome. Biomed Central (BMC) Genomics. 11:113. Interpretive Summary: The so-called 'jumping genes' (Transposable Elements (TEs)) play an important role in generating genetic diversity in plants. Genetic diversity is the cornerstone of agronomic improvement. Few plant species of agronomic importance have had indepth analyses of the TEs inhabiting their DNA. In this study the authors took advantage of the recently completed whole genome sequence of soybean to identify and characterize more than 32,000 unique TEs. They developed a database that permits the visualization and comparison of these elements. This is the largest compilation of TEs and most comprehensive curated database for any plant species. This data and associated database will permit scientists and students to study the evolution of a complex genome and the role of TEs in agricultural diversity. The addition of this knowledge to our understanding of complex traits may improve breeding strategies thus resulting in higher yield and better quality products.
Technical Abstract: The SoyTEdb provides resources and information related to transposable elements (TEs) in the soybean genome. The recent availability of the draft sequence of the soybean (Glycine max (L) Merr.) genome has allowed us to identify numerous TEs in this economically important legume crop. Using a combination of structure-based and homology-based approaches, a total of 32,552 retrotransposons (Class I) and 6,029 DNA transposons (Class II) with clear boundaries and insertion sites were structurally annotated and clearly categorized. The majority of these TEs (particular a few hundred low-copy number TE families) have not been previously described. These TE sequences have been anchored in and intergrated with the soybean physical map and genetic map, and are browsable and visualizable at any scale along the 20 soybean chromosomes, along with predicted genes and other sequence annotations. BLAST search and other infrastracture tools were implemented to facilitate annotation of TEs from soybean and other related legume species. All TEs or subsets of TEs can be downloaded from the database website http://www.soytedb.org. SoyTEdb represents the most comprehensive and the largest manually curated TE database for any individual plant genome completely sequenced to date, and will facilitate the studies of genome evolution, gene-TE interaction, and epigenomics in legumes and other plant species.