A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes
A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes
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DOI：
10.1111/j.1469-8137.2006.01662.x
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发表时间：
2006-01-01
期刊：
影响因子：
9.4
通讯作者：
Broadley, MR
中科院分区：
文献类型：
--
作者：
Hammond, JP;Bowen, HC;Broadley, MR
全基因组转录组分析揭示了生物系统如何在转录水平上进行调控。本研究报告了一种稳健的方法，使用Affymetrix Arabidopsis thaliana AT 1 -121501基因芯片（R）阵列对两种非模式植物物种（锌超积累植物Thlaspi caerulescens和非超积累植物Thlaspi arvense）的转录组进行分析和比较在两个物种的琼脂和堆肥生长的植物的芽中定量转录物丰度。基于Thlaspi gDNA与相应A. thaliana probes.基因芯片探针与Thlaspi基因序列的计算机比对和定量实时PCR证实了这种方法的有效性。caerulescens与T.未来对这些近缘物种地上部差异表达基因的功能分析将有助于我们更好地理解锌超积累的分子机制。
Whole-genome transcriptome profiling is revealing how biological systems are regulated at the transcriptional level. This study reports the development of a robust method to profile and compare the transcriptomes of two nonmodel plant species, Thlaspi caerulescens, a zinc (Zn) hyperaccumulator, and Thlaspi arvense, a nonhyperaccumulator, using Affymetrix Arabidopsis thaliana ATH1-121501 GeneChip (R) arrays (Affymetrix, Santa Clara, CA, USA).Transcript abundance was quantified in the shoots of agar- and compost-grown plants of both species. Analyses were optimized using a genomic DNA (gDNA)-based probe-selection strategy based on the hybridization efficiency of Thlaspi gDNA with corresponding A. thaliana probes. In silico alignments of GeneChip (R) probes with Thlaspi gene sequences, and quantitative real-time PCR, confirmed the validity of this approach.Approximately 5000 genes were differentially expressed in the shoots of T. caerulescens compared with T. arvense, including genes involved in Zn transport and compartmentalization.Future functional analyses of genes identified as differentially expressed in the shoots of these closely related species will improve our understanding of the molecular mechanisms of Zn hyperaccumulation.