title: GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii).
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.
  
  
  
  http://www.grtedb.org/.
authors.affiliation: Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Zhenzhen
authors.initials: Z
authors.lastname: Xu
authors.affiliation: Provincial Key Laboratory of Agrobiology, The Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Liu
authors.affiliation: Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Wanchao
authors.initials: W
authors.lastname: Ni
authors.affiliation: Provincial Key Laboratory of Agrobiology, The Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Peng
authors.affiliation: Provincial Key Laboratory of Agrobiology, The Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Cotton Biology, The Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
authors.forename: Wuwei
authors.initials: W
authors.lastname: Ye
authors.affiliation: Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Huang
authors.affiliation: Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Xianggui
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Xu
authors.affiliation: Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Guo
authors.affiliation: Key Laboratory of Cotton and Rapeseed (Nanjing), The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Xinlian
authors.initials: X
authors.lastname: Shen
authors.affiliation: Provincial Key Laboratory of Agrobiology, The Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Jianchang
authors.initials: J
authors.lastname: Du
mesh_terms: D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics; D030561:Databases, Nucleic Acid; D004171:Diploidy; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D020407:Internet; D057891:Tetraploidy; D064878:Web Browser
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant