RiTE database: a resource database for genus-wide rice genomics and evolutionary biology

BMC Genomics

Methodology Article

Carlos E. Maldonado L.¹  Jianwei Zhang¹  Dario Copetti²  Rod A. Wing²  Scott A. Jackson³  Dongying Gao³  Elena Barghini⁴  Chuanzhu Fan⁵  Jun Wang⁵  Andrea Zuccolo⁶  Rosa M. Cossu⁶  Stefan Roffler⁷  Thomas Wicker⁷  Yue-ie Hsing⁸  Olivier Panaud⁹  Moaine El Baidouri^1,10  Bin Han^1,11  Nori Kurata^1,12  Hajime Ohyanagi^1,12  Antonio Costa de Oliveira^1,13  Robert Henry^1,14  Angelina Angelova^1,15  Wen Wang^1,16  Mingsheng Chen^1,17 

[1] Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, 85721, Tucson, AZ, United States;Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, 85721, Tucson, AZ, United States;International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines;Center for Applied Genetic Technologies, University of Georgia, 30602, Athens, GA, United States;Department of Agriculture, Food, and Environment, University of Pisa, 56124, Pisa, Italy;Department of Biological Sciences, Wayne State University, 48202, Detroit, MI, United States;Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127, Pisa, Italy;Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland;Institute of Plant and Microbial Biology, Academia Sinica, Nankang, 11529, Taipei, Taiwan;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;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;Center for Applied Genetic Technologies, University of Georgia, 30602, Athens, GA, United States;National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 100029, Beijing, China;Plant Genetics Laboratory, National Institute of Genetics, 411-8540, Mishima, Shizuoka, Japan;Plant Genomics and Breeding Center, Federal University of Pelotas, Pelotas-RS, Brazil;Queensland Alliance for Agriculture and Food Innovation, University of Queensland, QLD 4072, Brisbane, Australia;School of Life Sciences, Heriot-Watt University, EH14 4AS, Edinburgh, Scotland;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, 650223, Kunming, Yunnan, China;State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, 100101, Beijing, China;

关键词: Rice;    Oryza;    Transposable elements;    Repeats;    Genome;    RiTE-db;   

DOI  :  10.1186/s12864-015-1762-3

 received in 2015-03-11, accepted in 2015-07-09,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundComparative 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.ResultsHere 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.ConclusionsThis 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.

【 授权许可】

Unknown   
© Copetti et al. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.