Transcript profiling during the early development of the maize brace root via Solexa sequencing
Transcript profiling during the early development of the maize brace root via Solexa sequencing
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通过 Solexa 测序对玉米大根早期发育过程中的转录本进行分析
DOI：
10.1111/j.1742-4658.2010.07941.x
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发表时间：
2011-01-01
期刊：
影响因子：
5.4
通讯作者：
Zheng, Cheng-Chao
中科院分区：
文献类型：
--
作者：
Li, Yan-Jie;Fu, Ya-Ru;Zheng, Cheng-Chao
目前，玉米支根早期发育的分子调控机制尚不清楚。为了深入了解与其发育相关的转录组动力学，Solexa测序公司（Illumina Inc., San Diego， CA， USA）进行了全基因组基因表达谱分析。从没有和刚刚出现支根的茎节点组织中产生了500多万个标签，其中两个库中分别有149 524个和178 131个干净标签。其中与内参基因匹配的标签分别为82 864个（55.4%）和91 678个（51.5%）。进一步分析log(2)比值为> 2或< -2 （P < 0.001）的差异表达最多的标签，除未知转录本外，共代表143个上调基因和152个下调基因，共分为11个功能类别。代谢、信号转导和细胞运输是最丰富的类别。在支撑根和侧根或不定根发育过程中发现了许多共同的基因或生物学途径，如参与细胞壁降解和合成、生长素运输和信号传导、乙烯信号传导等。接下来，对20个基因进行实时荧光定量PCR分析，结果与Solexa分析结果基本一致。此外，我们还比较了支撑根与玉米主根的转录组，发现在表达转录物的种类和丰度上存在显著差异。总之，我们首先揭示了玉米支根发育早期转录组的复杂变化，并提供了一套全面的数据，这对理解其分子调控至关重要。
Currently, the molecular regulation mechanisms involved in the early development of maize brace root are poorly known. To gain insight into the transcriptome dynamics that are associated with its development, genome-wide gene expression profiling was conducted by Solexa sequencing (Illumina Inc., San Diego, CA, USA). More than five million tags were generated from the stem node tissues without and with just-emerged brace roots, including 149 524 and 178 131 clean tags in the two libraries, respectively. Of these, 82 864 (55.4%) and 91 678 (51.5%) tags were matched to the reference genes. The most differentially expressed tags with a log(2) ratio > 2 or < -2 (P < 0.001) were analyzed further, representing 143 up-regulated and 152 down-regulated genes, except for unknown transcripts, which were classified into 11 functional categories. The most enriched categories were those of metabolism, signal transduction and cellular transport. Many genes or biological pathways were found to be commonly shared between brace root and lateral or adventitious root development, such as genes participating in cell wall degradation and synthesis, auxin transport and signaling, ethylene signaling, etc. Next, the expression patterns of 20 genes were assessed by quantitative real-time PCR, and the results obtained showed general agreement with the Solexa analysis. Furthermore, a comparison of the brace root transcriptome with that of maize primary root revealed substantial differences in the categories and abundances of expressed transcripts. In conclusion, we first reveal the complex changes in the transcriptome during the early development of maize brace root and provide a comprehensive set of data that are essential for understanding its molecular regulation.