A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
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DOI：
10.1101/gr.3657405
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发表时间：
2005-09-01
期刊：
影响因子：
7
通讯作者：
Wang, J
中科院分区：
文献类型：
--
作者：
Ma, LG;Chen, C;Wang, J
拟南芥和水稻是目前仅有的两种完成期基因组序列的模式植物。在这里，我们报告了基于目前已知的和预测的水稻基因组基因模型的低聚物微阵列的构建。该芯片用于分析这些基因模型在代表性水稻器官类型中的转录活性。在41754个已知和预测的基因模型中，有86%被检测到表达。这些表达的基因模型中有很大一部分被组织成染色体区域，长度约为100 kb，表现出共表达模式。与类似的拟南芥转录组全基因组调查相比，我们的研究结果表明，这两个基因组在其相应的器官类型中表达的比例相似。大量缺乏拟南芥同源基因的水稻基因模型得以表达。此外，水稻和拟南芥最匹配同源基因在不同功能群中的表达模式表明，它们在两个物种之间的保护程度存在显著差异。因此，这一初步的比较分析揭示了拟南芥和水稻转录组之间的一些基本相似性和差异性。
Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently known and predicted gene models in the rice genome. This microarray was used to analyze the transcriptional activity of the gene models in representative rice organ types. Expression of 86% of the 41,754 known and predicted gene models was detected. A significant fraction of these expressed gene models are organized into chromosomal regions, about 100 kb in length, that exhibit a coexpression pattern. Compared with similar genome-wide surveys of the Arabidopsis transcriptome, our results indicate that similar proportions of the two genomes are expressed in their corresponding organ types. A large percentage of the rice gene models that lack significant Arabidopsis homologs are expressed. Furthermore, the expression patterns of rice and Arabidopsis best-matched homologous genes in distinct functional groups indicate dramatic differences in their degree of conservation between the two species. Thus, this initial comparative analysis reveals some basic similarities and differences between the Arabidopsis and rice transcriptomes.