Abstract
Although several diploid and tetroploid Gossypium species genomes have been sequenced, the well annotated web-based transposable elements (TEs) database is lacking. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the cotton genome, a comprehensive, specific, and user-friendly web-based database, Gossypium raimondii transposable elements database (GrTEdb), was constructed. A total of 14 332 TEs were structurally annotated and clearly categorized in G. raimondii genome, and these elements have been classified into seven distinct superfamilies based on the order of protein-coding domains, structures and/or sequence similarity, including 2929 Copia-like elements, 10 368 Gypsy-like elements, 299 L1, 12 Mutators, 435 PIF-Harbingers, 275 CACTAs and 14 Helitrons. Meanwhile, the web-based sequence browsing, searching, downloading and blast tool were implemented to help users easily and effectively to annotate the TEs or TE fragments in genomic sequences from G. raimondii and other closely related Gossypium species. GrTEdb provides resources and information related with TEs in G. raimondii, and will facilitate gene and genome analyses within or across Gossypium species, evaluating the impact of TEs on their host genomes, and investigating the potential interaction between TEs and protein-coding genes in Gossypium species. Database URL: http://www.grtedb.org/
Highlights
Transposable elements (TEs) are the most abundant DNA components in most characterized genomes of high eukaryotes [1]
Retrotransposons are further classified into two distinct orders, long terminal repeat (LTR)-retrotransposons (Ty1/Copia and Ty3/Gypsy) and non-LTR retrotransposons (LINE and SINE), whereas DNA transposons are traditionally separated into two main orders, terminal inverted repeat (TIR) (Tc1Mariner, hAT, Mutator, PIF/Harbinger and CACTA) and Helitron (Helitron) [2, 3]
We carried out the characterization of almost all families of TEs in G. raimondii genome using comprehensive methods, and constructed the G. raimondii transposable elements database (GrTEdb) in this study
Summary
Transposable elements (TEs) are the most abundant DNA components in most characterized genomes of high eukaryotes [1]. In the chromosomal region search page, users can retrieve the TEs for any one entire chromosome or in a defined window around either a chromosomal position or a gene model, and the detailed information of each retrieved TEs can be viewed and downloaded by clicking the hyperlinks provided on the page (Figure 3). This function can help users to locate TEs that surround the genes of. Please feel free to contact us if you have any suggestions and problems
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