Department of Sciences, Technologies and Grapevine and Wine Markets, University of Verona, Verona, Italy.
Plant Physiol. 2010 Apr;152(4):1787-95. doi: 10.1104/pp.109.149716. Epub 2010 Jan 29.
The development of massively parallel sequencing technologies enables the sequencing of total cDNA (RNA-Seq) to derive accurate measure of individual gene expression, differential splicing activity, and to discover novel regions of transcription, dramatically changing the way that the functional complexity of transcriptomes can be studied. Here we report on the first use of RNA-Seq to gain insight into the wide range of transcriptional responses that are associated with berry development in Vitis vinifera 'Corvina'. More than 59 million sequence reads, 36 to 44 bp in length, were generated from three developmental stages: post setting, véraison, and ripening. The sequence reads were aligned onto the 8.4-fold draft sequence of the Pinot Noir 40024 genome and then analyzed to measure gene expression levels, to detect alternative splicing events, and expressed single nucleotide polymorphisms. We detected 17,324 genes expressed during berry development, 6,695 of which were expressed in a stage-specific manner, suggesting differences in expression for genes in numerous functional categories and a significant transcriptional complexity. This exhaustive overview of gene expression dynamics demonstrates the utility of RNA-Seq for identifying single nucleotide polymorphisms and splice variants and for describing how plant transcriptomes change during development.
高通量测序技术的发展使得对总 cDNA（RNA-Seq）进行测序成为可能，从而能够准确衡量个体基因表达、差异剪接活性，并发现新的转录区域，这极大地改变了研究转录组功能复杂性的方式。在这里，我们报告了首次使用 RNA-Seq 来深入了解与葡萄品种 'Corvina' 的浆果发育相关的广泛转录反应。从三个发育阶段（后设定、转色和成熟）生成了超过 5900 万个 36 到 44 个碱基长的序列读段。这些序列读段被映射到 Pinot Noir 40024 基因组的 8.4 倍草图序列上，然后进行分析以测量基因表达水平、检测选择性剪接事件和表达的单核苷酸多态性。我们在浆果发育过程中检测到 17324 个基因表达，其中 6695 个基因以阶段特异性方式表达，这表明许多功能类别中的基因表达存在差异，转录复杂性显著。这种对基因表达动态的全面概述证明了 RNA-Seq 用于识别单核苷酸多态性和剪接变体以及描述植物转录组在发育过程中如何变化的有效性。
