title: RiTE database: a resource database for genus-wide rice genomics and evolutionary biology.
abstract: 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.
authors.affiliation: Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States. dcopetti@email.arizona.edu.|International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines. dcopetti@email.arizona.edu.
authors.forename: Dario
authors.initials: D
authors.lastname: Copetti
authors.affiliation: Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States. zhangjw@email.arizona.edu.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860, Perpignan, France. moaine.elbaidouri@gmail.com.|Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States. moaine.elbaidouri@gmail.com.
authors.forename: Moaine
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authors.lastname: El Baidouri
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States. dgao@uga.edu.
authors.forename: Dongying
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authors.lastname: Gao
authors.affiliation: Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, United States. wangj@wayne.edu.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Agriculture, Food, and Environment, University of Pisa, 56124, Pisa, Italy. elena.barghini@gmail.com.
authors.forename: Elena
authors.initials: E
authors.lastname: Barghini
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127, Pisa, Italy. rosa.cossu@gmail.com.
authors.forename: Rosa M
authors.initials: RM
authors.lastname: Cossu
authors.affiliation: School of Life Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, Scotland. angelova@email.arizona.edu.
authors.forename: Angelina
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authors.affiliation: Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States. ceml@email.arizona.edu.
authors.forename: Carlos E
authors.initials: CE
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authors.affiliation: Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland. stefan.roffler@access.uzh.ch.
authors.forename: Stefan
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authors.affiliation: Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan. hohyanag@nig.ac.jp.
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authors.affiliation: Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland. wicker@botinst.uzh.ch.
authors.forename: Thomas
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authors.lastname: Wicker
authors.affiliation: Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, United States. cfan@wayne.edu.
authors.forename: Chuanzhu
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authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127, Pisa, Italy. a.zuccolo@sssup.it.
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authors.lastname: Zuccolo
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing, 100101, China. mschen@genetics.ac.cn.
authors.forename: Mingsheng
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authors.lastname: Chen
authors.affiliation: Plant Genomics and Breeding Center, Federal University of Pelotas, Pelotas-RS, Brazil. antonio.oliveira@pq.cnpq.br.
authors.forename: Antonio
authors.initials: A
authors.lastname: Costa de Oliveira
authors.affiliation: National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Beijing, 100029, China. bhan@ncgr.ac.cn.
authors.forename: Bin
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authors.lastname: Han
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia. robert.henry@uq.edu.au.
authors.forename: Robert
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authors.lastname: Henry
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan. bohsing@gate.sinica.edu.tw.
authors.forename: Yue-Ie
authors.initials: YI
authors.lastname: Hsing
authors.affiliation: Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan. nkurata@nig.ac.jp.
authors.forename: Nori
authors.initials: N
authors.lastname: Kurata
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China. wwang@mail.kiz.ac.cn.
authors.forename: Wen
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authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States. sjackson@uga.edu.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860, Perpignan, France. panaud@univ-perp.fr.
authors.forename: Olivier
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authors.affiliation: Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States. rwing@email.arizona.edu.|International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines. rwing@email.arizona.edu.
authors.forename: Rod A
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mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics; D030541:Databases, Genetic; D019143:Evolution, Molecular; D018745:Genome, Plant; D023281:Genomics; D012275:Oryza / Q000235:genetics*; D012984:Software
chemical_list: D004251:DNA Transposable Elements