Comparative transcriptomics reveals cryptic physiological differences between two accessions in Rorippa aquatica (Brassicaceae), North American Lake cress

Natural variation of wild plant species is a valuable genetic resource to reveal the plant and environmental interactions because such variations sometimes might be result of local adaptation. Rorippa aquatica (Brassicaceae) is a semi-aquatic plant showing leaf form alteration in response to surrounding environmental cues which is called heterophylly. Some habitats of R. aquatica are found in North America, and there are some accessions that show morphological differences, however, physiological differences between them are still unknown. Here, we surveyed the transcriptome response of the two R. aquatica accessions to reveal the cryptic physiological differences between the accessions. We first reconstructed Rorippa phylogeny with 47 species in the genus to confirm relationship between the accessions. Then, we performed large scale RNA-seq and de novo assembled them into 87, 754 unigenes, which were then extensively annotated by comparing to different databases. Results of principal component analysis and a self-organizing map suggested that photosynthetic activity is different between the accessions. Indeed, we showed that photosynthetic activity such as electron transport rate and the level of the redox state of the plastoquinone pool are different between accessions. These results indicated that one of the accessions may adapt to their habitat and comparative transcriptomics is effective method to find cryptic differences between closely related accessions.