GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii)
文献类型： 外文期刊
作者： Xu, Zhenzhen 1 ; Liu, Jing 1 ; Ni, Wanchao 1 ; Peng, Zhen 1 ; Guo, Yue 1 ; Ye, Wuwei 1 ; Huang, Fang 1 ; Zhang, Xianggui 1 ; Xu, Peng 1 ; Guo, Qi 1 ; Shen, Xinlian 4 ; Du, Jianchang 3 ;
作者机构： 1.Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
2.Provincial Key Laboratory of Agrobiology, The Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
3.Jiangsu Acad Agr Sci, Inst Biotechnol, Prov Key Lab Agrobiol, Nanjing 210014, Peoples R China
4.;Jiangsu Acad Agr Sci, Inst Ind Crops, Key Lab Cotton & Rapeseed Nanjing, Nanjing 210014, Peoples R China
5.State Key Laboratory of Cotton Biology, The Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
期刊名称：DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION （ 影响因子：3.451； 五年影响因子：4.159 ）
ISSN： 1758-0463
年卷期： 2017 年
页码：
收录情况： SCI
摘要： 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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