An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants
An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants
复制标题
DOI：
10.1111/j.1365-313x.2010.04222.x
复制
发表时间：
2010-07-01
期刊：
影响因子：
7.2
通讯作者：
Stacey, Gary
中科院分区：
文献类型：
--
作者：
Libault, Marc;Farmer, Andrew;Stacey, Gary
大豆（Glycine max L.）是一种主要作物，提供蛋白质和油的重要来源，也可以转化为生物柴油。大豆研究的一个重要里程碑是最近对其基因组进行了测序。该序列预测了69145个大豆基因，其中46430个预测具有高置信度。为了检查这些基因的表达，我们利用Illumina Solexa平台对来自14种条件（组织）的cDNA进行测序。结果是可通过浏览器（http：//digbio.missouri.edu/soybean_atlas）访问的可搜索大豆基因表达图谱。这些数据为55616个注释基因的转录提供了实验支持，也证明了13529个注释的大豆基因是假定的假基因，1736个目前未注释的序列被转录。对该图谱的分析揭示了不同组织之间基因表达模式的强烈差异，特别是根和气生器官之间的差异，但也揭示了其他组织中基因表达的相似性，如花和叶器官。为了证明该图谱的全部效用，我们使用Solexa序列数据和大规模qRT-PCR研究了参与转录的基因以及转录因子的表达模式。大豆基因表达图谱的可用性允许与记录在两个模式豆科植物物种中的基因表达进行比较，苜蓿和百脉根，以及拟南芥的可用数据，促进大豆研究的基础和应用方面。
P>Soybean (Glycine max L.) is a major crop providing an important source of protein and oil, which can also be converted into biodiesel. A major milestone in soybean research was the recent sequencing of its genome. The sequence predicts 69 145 putative soybean genes, with 46 430 predicted with high confidence. In order to examine the expression of these genes, we utilized the Illumina Solexa platform to sequence cDNA derived from 14 conditions (tissues). The result is a searchable soybean gene expression atlas accessible through a browser (http://digbio.missouri.edu/soybean_atlas). The data provide experimental support for the transcription of 55 616 annotated genes and also demonstrate that 13 529 annotated soybean genes are putative pseudogenes, and 1736 currently unannotated sequences are transcribed. An analysis of this atlas reveals strong differences in gene expression patterns between different tissues, especially between root and aerial organs, but also reveals similarities between gene expression in other tissues, such as flower and leaf organs. In order to demonstrate the full utility of the atlas, we investigated the expression patterns of genes implicated in nodulation, and also transcription factors, using both the Solexa sequence data and large-scale qRT-PCR. The availability of the soybean gene expression atlas allowed a comparison with gene expression documented in the two model legume species, Medicago truncatula and Lotus japonicus, as well as data available for Arabidopsis thaliana, facilitating both basic and applied aspects of soybean research.