A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling
A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling
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DOI：
10.1111/tpj.13312
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发表时间：
2016-12-01
期刊：
影响因子：
7.2
通讯作者：
Penin, Aleksey A.
中科院分区：
文献类型：
--
作者：
Klepikova, Anna V.;Kasianov, Artem S.;Penin, Aleksey A.
拟南芥（Arabidopsis thaliana）是植物分子生物学、遗传学和基因组学研究的一种模式植物。拟南芥基因的功能为提出假设和设计涉及其他植物，包括重要经济物种的实验提供了基础。对A.因此，对拟南芥基因组及其相关基因表达的详细而准确的了解对于基础研究和实际应用都非常重要。这一目标依赖于开发新的遗传和基因组资源，涉及新的数据采集和分析方法。我们在这里提出的全基因组分析A。使用高通量转录组测序的不同器官和发育阶段的拟南芥基因表达谱。25 706蛋白编码基因的表达，以及它们的稳定性和时空特异性，在79个器官和发育阶段进行了评估。对可变剪接事件的搜索确定了37873个以前未报道的剪接点，其中约30%发生在基因间区域。这些潜在地代表未包括在TAIR 10数据库中的新剪接基因。这些数据保存在开放访问的基于网络的数据库TraVA（转录组变异分析，http：//travadb.org/）中，其允许可视化和分析基因表达谱以及器官和发育阶段之间的差异基因表达。
Arabidopsis thaliana is a long established model species for plant molecular biology, genetics and genomics, and studies of A. thaliana gene function provide the basis for formulating hypotheses and designing experiments involving other plants, including economically important species. A comprehensive understanding of the A. thaliana genome and a detailed and accurate understanding of the expression of its associated genes is therefore of great importance for both fundamental research and practical applications. Such goal is reliant on the development of new genetic and genomic resources, involving new methods of data acquisition and analysis. We present here the genome-wide analysis of A. thaliana gene expression profiles across different organs and developmental stages using high-throughput transcriptome sequencing. The expression of 25 706 protein-coding genes, as well as their stability and their spatiotemporal specificity, was assessed in 79 organs and developmental stages. A search for alternative splicing events identified 37 873 previously unreported splice junctions, approximately 30% of them occurred in intergenic regions. These potentially represent novel spliced genes that are not included in the TAIR10 database. These data are housed in an open-access web-based database, TraVA (Transcriptome Variation Analysis, http://travadb.org/), which allows visualization and analysis of gene expression profiles and differential gene expression between organs and developmental stages.