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. 2015 Jul 22;16(1):538.
doi: 10.1186/s12864-015-1762-3.

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

Dario Copetti  1   2 , Jianwei Zhang  3 , Moaine El Baidouri  4   5 , Dongying Gao  6 , Jun Wang  7 , Elena Barghini  8 , Rosa M Cossu  9 , Angelina Angelova  10 , Carlos E Maldonado L  11 , Stefan Roffler  12 , Hajime Ohyanagi  13 , Thomas Wicker  14 , Chuanzhu Fan  15 , Andrea Zuccolo  16 , Mingsheng Chen  17 , Antonio Costa de Oliveira  18 , Bin Han  19 , Robert Henry  20 , Yue-Ie Hsing  21 , Nori Kurata  22 , Wen Wang  23 , Scott A Jackson  24 , Olivier Panaud  25 , Rod A Wing  26   27
Affiliations

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

Dario Copetti et al. BMC Genomics. .

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.

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Figures

Fig. 1
Fig. 1
Structure of the Rice TE database. The Rice TE database (RiTE-db) is composed of three data sets: publicly characterized TEs and repeats, de novo repeat libraries, and full-length elements isolated from genome assemblies. Result can be downloaded for the users' needs or used to build custom database quires for BLAST searches
Fig. 2
Fig. 2
RiTE database search function. Four main classifiers and checkboxes allow for the customization of search parameters (a), that are listed and visualized (b). Search results can be used as a dynamic BLAST database (c) or downloaded locally by using the links provided in via email
Fig. 3
Fig. 3
The RiTE database BLAST function. A query sequence can be aligned to the entire RiTE-db or to a customized subset of sequences. Alignment parameters can be tuned and the results can be visualized as pairwise alignments or in a tabular format
See this image and copyright information in PMC

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