DPTEdb, an integrative database of transposable elements in dioecious plants.

Shu-Fen Li,Jin-Hong Yuan,Guo-Jun Zhang,Xue-Jin Zhang,Chuan-Liang Deng,Lian-Feng Gu,Wu-Jun Gao

doi:10.1093/database/baw078

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

Highlights

Transposable elements (TEs) are DNA elements that are capable of moving from one place in the genome to another
Using the methods described earlier, a total of 31 340 TEs belonging to 3446 TE families were identified in the eight dioecious plant genomes
A total of 2458, 5622, 11 673, 7071 and 4038 TEs were detected from the entire genome sequences of C. papaya, C. sativa, P. trichocarpa, M. notabilis and P. dactylifera, respectively

Summary

Introduction

Transposable elements (TEs) are DNA elements that are capable of moving from one place in the genome to another. They contribute greatly to eukaryotic genomes, plant genomes, and can account for up to 90% of the genome size in several plant species [1, 2]. TEs are classified into two classes based on their mode of transposition. Class I elements are known as retrotransposons that propagate via an RNA intermediate. These elements use a ‘copy and paste’ mechanism to insert themselves into a new location in the genome. DNA transposons are further classified into three main subclasses, namely, terminal inverted repeats (TIRs), Helitrons and Mavericks [4]

Results

Discussion

Conclusion