Sinbase: An Integrated Database to Study Genomics, Genetics and Comparative Genomics in Sesamum indicum
Sinbase: An Integrated Database to Study Genomics, Genetics and Comparative Genomics in Sesamum indicum
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DOI：
10.1093/pcp/pcu175
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发表时间：
2015-01-01
影响因子：
4.9
通讯作者：
Zhang, Xiurong
中科院分区：
文献类型：
--
作者：
Wang, Linhai;Yu, Jingyin;Zhang, Xiurong
芝麻（Sesamum indicum L.）是一种古老而重要的油料作物，广泛种植于热带和亚热带地区。它属于巨大的 Lamiales 目，其中包括许多著名或经济上重要的物种，如橄榄 (Olea europaea)、益母草 (Leonurus japonicus) 和薰衣草 (Lavandula spica)，其中许多具有重要的药理特性。尽管它们很重要，但由于缺乏参考基因组信息，对这些物种的遗传和基因组分析还不够。现有的印度S. indicum基因组将为研究S. indicum遗传性状和比较基因组学提供前所未有的机会。为了向全球研究界提供 S. indicum 基因组信息，我们设计了 Sinbase，这是一个基于网络的数据库，包含全面的芝麻基因组、遗传和比较基因组信息。 Sinbase 包括组装的芝麻伪分子染色体、蛋白质编码基因 (27,148)、转座元件 (372,167) 和非编码 RNA (1,748) 的序列。特别是，Sinbase 提供了有关各种植物基因组共线区域的独特且有价值的信息，包括拟南芥、大豆、葡萄和番茄。 Sinbase还提供了有用的搜索功能和数据挖掘工具，包括关键字搜索和本地BLAST服务。 Sinbase 将定期更新新功能、基因组注释改进和新基因组序列，并可在 http://ocri-genomics.org/Sinbase/ 上免费访问。
Sesame (Sesamum indicum L.) is an ancient and important oilseed crop grown widely in tropical and subtropical areas. It belongs to the gigantic order Lamiales, which includes many well-known or economically important species, such as olive (Olea europaea), leonurus (Leonurus japonicus) and lavender (Lavandula spica), many of which have important pharmacological properties. Despite their importance, genetic and genomic analyses on these species have been insufficient due to a lack of reference genome information. The now available S. indicum genome will provide an unprecedented opportunity for studying both S. indicum genetic traits and comparative genomics. To deliver S. indicum genomic information to the worldwide research community, we designed Sinbase, a web-based database with comprehensive sesame genomic, genetic and comparative genomic information. Sinbase includes sequences of assembled sesame pseudomolecular chromosomes, protein-coding genes (27,148), transposable elements (372,167) and non-coding RNAs (1,748). In particular, Sinbase provides unique and valuable information on colinear regions with various plant genomes, including Arabidopsis thaliana, Glycine max, Vitis vinifera and Solanum lycopersicum. Sinbase also provides a useful search function and data mining tools, including a keyword search and local BLAST service. Sinbase will be updated regularly with new features, improvements to genome annotation and new genomic sequences, and is freely accessible at http://ocri-genomics.org/Sinbase/.