RiTE database: a resource database for genus-wide rice genomics and evolutionary biology.
RiTE database: a resource database for genus-wide rice genomics and evolutionary biology.
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DOI：
10.1186/s12864-015-1762-3
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发表时间：
2015-07-22
期刊：
影响因子：
4.4
通讯作者：
Wing RA
中科院分区：
文献类型：
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作者：
Copetti D;Zhang J;El Baidouri M;Gao D;Wang J;Barghini E;Cossu RM;Angelova A;Maldonado L CE;Roffler S;Ohyanagi H;Wicker T;Fan C;Zuccolo A;Chen M;Costa de Oliveira A;Han B;Henry R;Hsing YI;Kurata N;Wang W;Jackson SA;Panaud O;Wing RA
全基因组的比较进化分析不仅需要精确的基因空间注释，而且还需要适当的注释的重复部分，这往往是最大的组成部分，如果不是所有的基因组大于50 kb的大小。在这里，我们提出了水稻TE数据库（RiTE-db）-转座因子和重复序列在11个二倍体物种的属稻属和密切相关的外组Leersia perrieri的属范围内的集合。该数据库由超过170，000个条目组成，分为三种主要类型：（i）一组分类和策划的公开重复序列，（ii）一组从12个物种的基因组测序调查中获得的高度重复序列的共识组件;以及（iii）一组从12个全基因组组件中识别和提取的全长TE。这是第一次报告的重复数据集，跨越整个属内的重复变异的大部分，其中包括完整的元素以及未组装的重复。该数据库允许序列浏览、下载和相似性搜索。由于所采用的策略，RiTE-db开辟了一条前所未有的直接比较研究的新途径，这些研究跨越了1500万年的稻属多样性的整个核重复内容。本文的在线版本（doi：10.1186/s12864-015-1762-3）包含补充材料，可供授权用户使用。
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. The online version of this article (doi:10.1186/s12864-015-1762-3) contains supplementary material, which is available to authorized users.