BACKGROUND: Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. RESULTS: Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. CONCLUSIONS: This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.
| Identifer | oai:union.ndltd.org:arizona.edu/oai:arizona.openrepository.com:10150/610281 |
| Date | January 2015 |
| Creators | Copetti, Dario, Zhang, Jianwei, El Baidouri, Moaine, Gao, Dongying, Wang, Jun, Barghini, Elena, Cossu, Rosa M., Angelova, Angelina, Maldonado L., Carlos E., Roffler, Stefan, Ohyanagi, Hajime, Wicker, Thomas, Fan, Chuanzhu, Zuccolo, Andrea, Chen, Mingsheng, Costa de Oliveira, Antonio, Han, Bin, Henry, Robert, Hsing, Yue-ie, Kurata, Nori, Wang, Wen, Jackson, Scott A., Panaud, Olivier, Wing, Rod A. |
| Contributors | Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, International Rice Research Institute, Genetic Resource Center, Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, Center for Applied Genetic Technologies, University of Georgia, Department of Biological Sciences, Wayne State University, Department of Agriculture, Food, and Environment, University of Pisa, Institute of Life Sciences, Scuola Superiore Sant’Anna, School of Life Sciences, Heriot-Watt University, Institute of Plant Biology, University of Zürich, Plant Genetics Laboratory, National Institute of Genetics, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Plant Genomics and Breeding Center, Federal University of Pelotas, National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Institute of Plant and Microbial Biology, Academia Sinica, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences |
| Publisher | BioMed Central Ltd |
| Source Sets | University of Arizona |
| Language | English |
| Detected Language | English |
| Type | Article |
| Rights | © 2015 Copetti et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0) |
| Relation | http://www.biomedcentral.com/1471-2164/16/538 |
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