GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii)

Publication Overview
TitleGrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii)
AuthorsXu Z, Liu J, Ni W, Peng Z, Guo Y, Ye W, Huang F, Zhang X, Xu P, Guo Q, Shen X, Du J
TypeJournal Article
Journal NameDatabase
Volume2017
Year2017
Page(s)bax013
CitationXu Z, Liu J, Ni W, Peng Z, Guo Y, Ye W, Huang F, Zhang X, Xu P, Guo Q, Shen X, Du J. GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii). Database, Volume 2017, 2017, bax013, doi.org/10.1093/database/bax013.
Publication CodeDBS-2017-bax013

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 proteincoding 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.
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Additional details for this publication include:
Property NameValue
Journal CodeDBS
LanguageEnglish
Publication CodeDBS-2017-bax013
URLhttps://academic.oup.com/database/article/doi/10.1093/database/bax013/3084694