Kansas State University, Department of Plant Pathology, Manhattan, KS, 66506, USA.
Colby-Sawyer College, Natural Sciences Department, New London, NH, 03257, USA.
Sci Rep. 2017 Aug 8;7(1):7567. doi: 10.1038/s41598-017-07866-6.
The evolution of phenotypes occurs through changes both in protein sequence and gene expression levels. Though much of plant morphological evolution can be explained by changes in gene expression, examining its evolution has challenges. To gain a new perspective on organ evolution in plants, we applied a phylotranscriptomics approach. We combined a phylostratigraphic approach with gene expression based on the strand-specific RNA-seq data from seedling, floral bud, and root of 19 Arabidopsis thaliana accessions to examine the age and sequence divergence of transcriptomes from these organs and how they adapted over time. Our results indicate that, among the sense and antisense transcriptomes of these organs, the sense transcriptomes of seedlings are the evolutionarily oldest across all accessions and are the most conserved in amino acid sequence for most accessions. In contrast, among the sense transcriptomes from these same organs, those from floral bud are evolutionarily youngest and least conserved in sequence for most accessions. Different organs have adaptive peaks at different stages in their evolutionary history; however, all three show a common adaptive signal from the Magnoliophyta to Brassicale stage. Our research highlights how phylotranscriptomic analyses can be used to trace organ evolution in the deep history of plant species.
表型的进化是通过蛋白质序列和基因表达水平的变化来实现的。虽然植物形态进化的很大一部分可以用基因表达的变化来解释，但研究其进化存在挑战。为了从新的角度研究植物器官的进化，我们采用了系统发生转录组学的方法。我们结合了系统发生地层学的方法和基于 strand-specific RNA-seq 数据的基因表达，这些数据来自 19 个拟南芥品系的幼苗、花芽和根，以研究这些器官的转录组的年龄和序列分化，以及它们随着时间的推移如何适应。我们的结果表明，在这些器官的 sense 和 antisense 转录组中，所有品系的幼苗 sense 转录组在进化上是最古老的，并且在大多数品系中在氨基酸序列上是最保守的。相比之下，在来自同一器官的 sense 转录组中，大多数品系的花芽 sense 转录组在进化上是最新的，在序列上是最不保守的。不同的器官在其进化历史的不同阶段有适应的高峰；然而，所有三个器官都显示出从木兰植物到 Brassicale 阶段的共同适应信号。我们的研究强调了系统发生转录组学分析如何用于追踪植物物种的深层历史中的器官进化。
