title: DPTEdb, an integrative database of transposable elements in dioecious plants.
abstract: Dioecious plants usually harbor 'young' sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants.Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php.
authors.affiliation: College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
authors.forename: Shu-Fen
authors.initials: SF
authors.lastname: Li
authors.affiliation: School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China.
authors.forename: Guo-Jun
authors.initials: GJ
authors.lastname: Zhang
authors.affiliation: College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
authors.forename: Xue-Jin
authors.initials: XJ
authors.lastname: Zhang
authors.affiliation: College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
authors.forename: Jin-Hong
authors.initials: JH
authors.lastname: Yuan
authors.affiliation: College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
authors.forename: Chuan-Liang
authors.initials: CL
authors.lastname: Deng
authors.affiliation: Basic Forestry and Proteomics Center, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, China gaowujun1@163.com lfgu@fafu.edu.cn.
authors.forename: Lian-Feng
authors.initials: LF
authors.lastname: Gu
authors.affiliation: College of Life Sciences, Henan Normal University, Xinxiang 453007, China gaowujun1@163.com lfgu@fafu.edu.cn.
authors.forename: Wu-Jun
authors.initials: WJ
authors.lastname: Gao
mesh_terms: D019295:Computational Biology; D004251:DNA Transposable Elements / Q000235:genetics*; D030541:Databases, Genetic; D018745:Genome, Plant / Q000235:genetics*; D020407:Internet; D010944:Plants / Q000235:genetics*; D014584:User-Computer Interface
chemical_list: D004251:DNA Transposable Elements