Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
BMC Genomics. 2013 Aug 28;14:578. doi: 10.1186/1471-2164-14-578.
The investigation of extremophile plant species growing in their natural environment offers certain advantages, chiefly that plants adapted to severe habitats have a repertoire of stress tolerance genes that are regulated to maximize plant performance under physiologically challenging conditions. Accordingly, transcriptome sequencing offers a powerful approach to address questions concerning the influence of natural habitat on the physiology of an organism. We used RNA sequencing of Eutrema salsugineum, an extremophile relative of Arabidopsis thaliana, to investigate the extent to which genetic variation and controlled versus natural environments contribute to differences between transcript profiles.
Using 10 million cDNA reads, we compared transcriptomes from two natural Eutrema accessions (originating from Yukon Territory, Canada and Shandong Province, China) grown under controlled conditions in cabinets and those from Yukon plants collected at a Yukon field site. We assessed the genetic heterogeneity between individuals using single-nucleotide polymorphisms (SNPs) and the expression patterns of 27,016 genes. Over 39,000 SNPs distinguish the Yukon from the Shandong accessions but only 4,475 SNPs differentiated transcriptomes of Yukon field plants from an inbred Yukon line. We found 2,989 genes that were differentially expressed between the three sample groups and multivariate statistical analyses showed that transcriptomes of individual plants from a Yukon field site were as reproducible as those from inbred plants grown under controlled conditions. Predicted functions based upon gene ontology classifications show that the transcriptomes of field plants were enriched by the differential expression of light- and stress-related genes, an observation consistent with the habitat where the plants were found.
Our expectation that comparative RNA-Seq analysis of transcriptomes from plants originating in natural habitats would be confounded by uncontrolled genetic and environmental factors was not borne out. Moreover, the transcriptome data shows little genetic variation between laboratory Yukon Eutrema plants and those found at a field site. Transcriptomes were reproducible and biological associations meaningful whether plants were grown in cabinets or found in the field. Thus RNA-Seq is a valuable approach to study native plants in natural environments and this technology can be exploited to discover new gene targets for improved crop performance under adverse conditions.
研究在自然环境中生长的极端植物物种具有一定的优势，主要是因为适应恶劣生境的植物具有一系列的应激耐受基因，这些基因的调节可以最大限度地提高植物在生理挑战条件下的表现。因此，转录组测序为研究自然栖息地对生物体生理的影响提供了一种强有力的方法。我们使用拟南芥的近亲盐芥(Eutrema salsugineum)的 RNA 测序来研究遗传变异以及受控环境与自然环境对转录谱差异的影响程度。
我们使用 1000 万个 cDNA 读取数，比较了在培养箱中生长的两个自然盐芥（分别来自加拿大育空地区和中国山东省）和在育空野外采集的盐芥的转录组。我们使用单核苷酸多态性（SNP）评估个体之间的遗传异质性，并对 27016 个基因的表达模式进行了评估。育空地区和山东地区的个体之间有超过 39000 个 SNP 区分，但只有 4475 个 SNP 区分了育空野外植物和育空自交系的转录组。我们发现了 2989 个在三个样本组之间差异表达的基因，多元统计分析表明，育空野外植物个体的转录组与在受控条件下生长的自交植物的转录组一样具有可重复性。基于基因本体分类的预测功能表明，野外植物的转录组通过差异表达的光和应激相关基因而富集，这一观察结果与植物所在的栖息地一致。
我们预期对源自自然栖息地的植物的转录组进行比较 RNA-Seq 分析会受到不受控制的遗传和环境因素的干扰，但事实并非如此。此外，实验室育空盐芥植物和野外发现的盐芥植物之间的转录组遗传差异很小。无论是在培养箱中生长的植物还是在野外发现的植物，转录组都具有可重复性和生物学相关性。因此，RNA-Seq 是研究自然环境中本地植物的一种有价值的方法，这项技术可以用于发现新的基因靶点，以提高作物在不利条件下的性能。
