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

BMC Genomics

Rod A. Wing⁹  Olivier Panaud³  Scott A. Jackson^1,14  Wen Wang^1,16  Nori Kurata^1,13  Yue-ie Hsing⁷  Robert Henry^1,15  Bin Han^1,10  Antonio Costa de Oliveira⁴  Mingsheng Chen⁵  Andrea Zuccolo^1,11  Chuanzhu Fan⁶  Thomas Wicker^1,12  Hajime Ohyanagi^1,13  Stefan Roffler^1,12  Carlos E. Maldonado L.²  Angelina Angelova¹  Rosa M. Cossu^1,11  Elena Barghini⁸  Jun Wang⁶  Dongying Gao^1,14  Moaine El Baidouri^1,14  Jianwei Zhang²  Dario Copetti⁹ 

[1] School of Life Sciences, Heriot-Watt University, Edinburgh EH14 4AS, Scotland;Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson 85721, AZ, United States;Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, Perpignan, 66860, France;Plant Genomics and Breeding Center, Federal University of Pelotas, Pelotas-RS, Brazil;State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing 100101, China;Department of Biological Sciences, Wayne State University, Detroit 48202, MI, United States;Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan;Department of Agriculture, Food, and Environment, University of Pisa, Pisa, 56124, Italy;International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines;National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Beijing 100029, China;Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, 56127, Italy;Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, Zürich, 8008, Switzerland;Plant Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Shizuoka, Japan;Center for Applied Genetic Technologies, University of Georgia, Athens 30602, GA, United States;Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia;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 650223, Yunnan, China

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

Others  :  1222463
DOI  :  10.1186/s12864-015-1762-3

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

【 摘 要 】

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.

【 授权许可】

   
2015 Copetti et al.

【 图 表 】

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