title: SoyTEdb: a comprehensive database of transposable elements in the soybean genome.
abstract: BACKGROUND
  Transposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their host genomes, but also play significant roles in regulating gene expression, altering gene function, and creating new genes. Thus, complete identification of transposable elements in sequenced genomes and construction of comprehensive transposable element databases are essential for accurate annotation of genes and other genomic components, for investigation of potential functional interaction between transposable elements and genes, and for study of genome evolution. The recent availability of the soybean genome sequence has provided an unprecedented opportunity for discovery, and structural and functional characterization of transposable elements in this economically important legume crop.
  
  
  METHODS
  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, and a soybean transposable element database, SoyTEdb, was established. These transposable elements have been anchored in and integrated 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 transposable elements or fragments from soybean and other related legume species. The majority (> 95%) of these elements (particularly a few hundred low-copy-number families) are first described in this study.
  
  
  CONCLUSIONS
  SoyTEdb provides resources and information related to transposable elements in the soybean genome, representing the most comprehensive and the largest manually curated transposable element database for any individual plant genome completely sequenced to date. Transposable elements previously identified in legumes, the third largest family of flowering plants, are relatively scarce. Thus this database will facilitate structural, evolutionary, functional, and epigenetic analyses of transposable elements in soybean and other legume species.
authors.affiliation: Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Jianchang
authors.initials: J
authors.lastname: Du
authors.forename: David
authors.initials: D
authors.lastname: Grant
authors.forename: Zhixi
authors.initials: Z
authors.lastname: Tian
authors.forename: Rex T
authors.initials: RT
authors.lastname: Nelson
authors.forename: Liucun
authors.initials: L
authors.lastname: Zhu
authors.forename: Randy C
authors.initials: RC
authors.lastname: Shoemaker
authors.forename: Jianxin
authors.initials: J
authors.lastname: Ma
mesh_terms: D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics; D030561:Databases, Nucleic Acid; D018745:Genome, Plant; D018626:Retroelements; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant; D018626:Retroelements