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

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, Nor, Wang, Wen, Jackson, Scott A., Panaud, Olivier and Wing, Rod A. (2015) RiTE database: A resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics, 16 1: 538-538. doi:10.1186/s12864-015-1762-3

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Author 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, Nor
Wang, Wen
Jackson, Scott A.
Panaud, Olivier
Wing, Rod A.
Title RiTE database: A resource database for genus-wide rice genomics and evolutionary biology
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2015-07-22
Year available 2015
Sub-type Article (original research)
DOI 10.1186/s12864-015-1762-3
Open Access Status File (Publisher version)
Volume 16
Issue 1
Start page 538
End page 538
Total pages 10
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2016
Language eng
Formatted abstract
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.

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.

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.
Keyword Genome
RiTE db
Transposable elements
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2016 Collection
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Citation counts: TR Web of Science Citation Count  Cited 3 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 3 times in Scopus Article | Citations
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Created: Tue, 28 Jul 2015, 01:36:23 EST by System User on behalf of Qld Alliance for Agriculture and Food Innovation