RiTE database: a resource database for genus-wide rice genomics and evolutionary biology
El Baidouri, Moaine
Cossu, Rosa M.
Maldonado L., Carlos E.
Costa de Oliveira, Antonio
Jackson, Scott A.
Wing, Rod A.
AffiliationArizona 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
MetadataShow full item record
PublisherBioMed Central Ltd
CitationCopetti et al. BMC Genomics (2015) 16:538 DOI 10.1186/s12864-015-1762-3
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).
Collection InformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at email@example.com.
AbstractBACKGROUND: 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.
VersionFinal published version
Except where otherwise noted, this item's license is described as © 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).