ArticleDatabase : the journal of biological databases and curation2016
DPTEdb, an integrative database of transposable elements in dioecious plants.
Article in Database : the journal of biological databases and curation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 23 citations in OpenAlex.
- CREATE: a novel attention-based framework for efficient classification of transposable elements.Briefings in bioinformatics · 2025Article
- PlantLTRdb: An interactive database for 195 plant species LTR-retrotransposons.Frontiers in plant science · 2023Article
- TransposonUltimate: software for transposon classification, annotation and detection.Nucleic acids research · 2022Article
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes.Scientific data · 2021Article
- Computational Analysis of Transposable Elements and CircRNAs in Plants.Methods in molecular biology (Clifton, N.J.) · 2021Article
- DeviaTE: Assembly-free analysis and visualization of mobile genetic element composition.Molecular ecology resources · 2019Article
- Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes.Molecular genetics and genomics : MGG · 2018Article
- Article
- Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes.Genome biology and evolution · 2017Article
- GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii).Database : the journal of biological databases and curation · 2017Article
- Article
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7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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