PT  - JOURNAL ARTICLE
AU  - Li Lei
AU  - Joshua G Steffen
AU  - Edward J Osborne
AU  - Christopher Toomajian
TI  - Plant organ evolution revealed by phylotranscriptomics in <em>Arabidopsis</em>
AID  - 10.1101/119511
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 119511
4099  - http://biorxiv.org/content/early/2017/03/22/119511.short
4100  - http://biorxiv.org/content/early/2017/03/22/119511.full
AB  - The evolution of species’ 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, from the Magnoliophyta stage to the Brassicale stage, all three organs show a common adaptive signal. Our research is significant because it offers novel evolutionary insight on plant organs revealed by phylotranscriptomics.