Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha

Abstract

The rhizome is a plant organ that develops from a shoot apical meristem but penetrates into belowground environments. To characterize the gene expression profile of rhizomes, we compared the rhizome transcriptome with those of the leaves, shoots and roots of a rhizomatous Brassicaceae plant, Cardamine leucantha. Overall, rhizome transcriptomes were characterized by the absence of genes that show rhizome-specific expression and expression profiles intermediate between those of shoots and roots. Our results suggest that both endogenous developmental factors and external environmental factors are important for controlling the rhizome transcriptome. Genes that showed relatively high expression in the rhizome compared to shoots and roots included those related to belowground defense, control of reactive oxygen species and cell elongation under dark conditions. A comparison of transcriptomes further allowed us to identify the presence of an ER body, a defense-related belowground organelle, in epidermal cells of the C. leucantha rhizome, which is the first report of ER bodies in rhizome tissue.

Figure 1

An illustration of four tissues (circles) collected from a current-year flowering shoot of a clonal rhizomatous plant, Cardamine leucantha (a), photographs of elongating belowground rhizomes (b), magnified view of a rhizome (c), floral bud and young leaves (d), rhizome tip and root (e) and tissue sections of a rhizome apex including its meristem (f,g). In (a), arrows indicate the direction of elongation of the current-year shoot, current-year rhizome and rhizome of the previous year and the dashed line represents the above- and belowground boundary. In (f) and (g), bars indicate scales and * and ** represent the corpus (Co) and tunica (Tu), respectively.

Figure 2

Principal component analysis (PCA) of transcriptome data of four tissues, i.e. rhizomes, shoots, roots and leaves of Cardamine leucantha (a). Spearman rank correlations between the C. leucantha transcriptome and Arabidopsis thaliana microarray (AtGenExpress) data for seven different tissues and developmental stages (b). In (a,b), red circles and blue triangles correspond to plants A and B, respectively. Shoot: vegetative_shoot_apex_7d, flower: flower_stage 10/11.

Figure 3

A heatmap of 16 k-mean clusters classified by relative expression patterns in four tissues, i.e. leaf, shoot, rhizome and root, of Cardamine leucantha plants A and B. Numbers of transcripts, annotated transcripts and enriched gene ontologies (GOs) for each cluster are also listed. Expression specificity based on the expression pattern is indicated by vertical bars.

Figure 4

Expression (log₂ FPKM) of six ER-body-related genes across four tissues (a), fluorescent microscope images of epidermal cells in the rhizome (b) and mature leaf (c), and a transmission electron microscope (TEM) image of an epidermal cell in the rhizome (d) of C. leucantha. In (a), red and blue circles represent plants A and B, respectively. In (b,c), GFP targeted to ER was transiently expressed. In (b,d), putative ER bodies are indicated by red arrows. Bars indicate ten micrometres in (b,c) and one micrometre in (d).