Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches.
Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches.
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Pará橡胶树基因组和多转录组数据库的构建加速了橡胶研究。
DOI：
10.1186/s12864-017-4333-y
复制
发表时间：
2018-01-19
期刊：
影响因子：
4.4
通讯作者：
Matsui M
中科院分区：
文献类型：
--
作者：
Makita Y;Kawashima M;Lau NS;Othman AS;Matsui M
天然橡胶是一种重要的经济材料。目前，帕拉橡胶树（Hevea brasiliensis）是主要的商业来源。人们对分子水平上的橡胶生物合成知之甚少。新一代测序 (NGS) 技术带来了三个橡胶品种的基因组草图和各种 RNA 测序 (RNA-seq) 数据。然而，目前没有按基因组织的基因组或转录组数据库（DB）。面向基因的数据库是橡胶研究的宝贵支持。基于我们最初的 H. brasiliensis RRIM600 基因组序列草案，我们构建了橡胶树基因组和转录组数据库。我们的数据库提供基因组信息，包括基因功能注释和 RNA-seq 的多转录组数据、全长 cDNA（包括 PacBio Isoform 测序 (Iso-Seq)）、EST 和源自 CAGE 技术的全基因组转录起始位点 (TSS)。使用我们原始且公开的 RNA-seq 数据，我们计算了共表达基因，用于识别功能相关的基因集和/或受相同转录因子 (TF) 调控的基因。用户可以通过面向基因的网页和基因组浏览器访问多转录组数据。对于基因搜索系统，我们提供关键词搜索、序列同源性搜索和基因表达搜索；用户还可以轻松选择自己的表达阈值。橡胶基因组和转录组数据库提供橡胶树基因组序列和多转录组数据。该数据库对于全面了解橡胶转录组很有用。这将有助于橡胶和经济上重要的近亲如 R. communis、M. esculenta 和 J. curcas 的工业和学术研究人员。 Rubber Transcriptome DB 版本 2017.03 可通过 http://matsui-lab.riken.jp/rubber/ 访问。本文的在线版本 (10.1186/s12864-017-4333-y) 包含补充材料，可供授权用户使用。
Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-generation sequencing (NGS) technologies brought draft genomes of three rubber cultivars and a variety of RNA sequencing (RNA-seq) data. However, no current genome or transcriptome databases (DB) are organized by gene. A gene-oriented database is a valuable support for rubber research. Based on our original draft genome sequence of H. brasiliensis RRIM600, we constructed a rubber tree genome and transcriptome DB. Our DB provides genome information including gene functional annotations and multi-transcriptome data of RNA-seq, full-length cDNAs including PacBio Isoform sequencing (Iso-Seq), ESTs and genome wide transcription start sites (TSSs) derived from CAGE technology. Using our original and publically available RNA-seq data, we calculated co-expressed genes for identifying functionally related gene sets and/or genes regulated by the same transcription factor (TF). Users can access multi-transcriptome data through both a gene-oriented web page and a genome browser. For the gene searching system, we provide keyword search, sequence homology search and gene expression search; users can also select their expression threshold easily. The rubber genome and transcriptome DB provides rubber tree genome sequence and multi-transcriptomics data. This DB is useful for comprehensive understanding of the rubber transcriptome. This will assist both industrial and academic researchers for rubber and economically important close relatives such as R. communis, M. esculenta and J. curcas. The Rubber Transcriptome DB release 2017.03 is accessible at http://matsui-lab.riken.jp/rubber/. The online version of this article (10.1186/s12864-017-4333-y) contains supplementary material, which is available to authorized users.
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DOI：
10.1093/dnares/dsw056
发表时间：
2017-04-01
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Makita Y;Ng KK;Veera Singham G;Kawashima M;Hirakawa H;Sato S;Othman AS;Matsui M
通讯作者：
Matsui M
影响因子：
12.3
作者：
Buels R;Yao E;Diesh CM;Hayes RD;Munoz-Torres M;Helt G;Goodstein DM;Elsik CG;Lewis SE;Stein L;Holmes IH
通讯作者：
Holmes IH
影响因子：
14.9
作者：
Clark K;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
Sayers EW
影响因子：
14.9
作者：
Kodama Y;Shumway M;Leinonen R;International Nucleotide Sequence Database Collaboration
通讯作者：
International Nucleotide Sequence Database Collaboration
影响因子：
4.9
作者：
Makita Y;Shimada S;Kawashima M;Kondou-Kuriyama T;Toyoda T;Matsui M
通讯作者：
Matsui M