SoyTEdb: a comprehensive database of transposable elements in the soybean genome

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.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.Transposable elements (TEs) are the most abundant genomic components in flowering plants. For example, approximately 40% of the rice genome [1] and 80% of the maize genome is occupied by TEs [2]. Based on transposition mechanisms, TEs are generally classified into two types: DNA transposons and retrotransposons. DNA elements in plants are further classified into at least seven superfamilies based on their structural features and transposase similarities, whereas retrotransposons are traditionally separated into two superfamilies, the long terminal repeat (LTR)-retrotransposons and