Figure 1.
The evolutionary and developmental context of siphonous morphology in Caulerpa taxifolia.
A) Evolutionary relationships among green algae with unicellular, siphonous, siphonocladous, and uninucleate multicellular lifestyles. Diagrams indicate body plan, redrawn from Cocquyt et al. [40]. B) The growing frond apex of Caulerpa taxifolia, producing young pinnules. C) Diagram of sampled regions. D) Principal Component Analysis (PCA) performed on organ RNA-Seq replicates based on transcript accumulation levels. 95% confidence ellipses are indicated for each sampled region. For convenience, a dotted line is provided separating apical from basal pseudo-organ types to relate data back to morphology. Colors indicate different sampled regions (as opposed to nodes in subsequent figures). Red, apex; orange, pinnules; yellow, rachis; green, frond base; blue, stolon; purple, holdfast.
Figure 2.
Intracellular accumulation of transcripts in a giant, single-celled organism.
A) Principal Component Analysis (PCA) performed on transcript accumulation across sampled regions (the inverse of the PCA presented in Fig. 1D). Four major densities in the transcript accumulation variance structure are indicated by arrow. B) PCA was performed to visualize results of clustering by transcripts using Self-Organizing Maps (SOMs), visualized as different colors corresponding to nodes. C) Transcript accumulation profiles of genes belonging to different nodes, arranged with increasing abundance in an apical-to-basal direction. Scaled transcript abundance is such that the average abundance level across pseudo-organs for each transcript is 0 and variance is equal to 1. Scaled transcript abundance is shown as a boxplot and individual genes as jittered points (randomly displaced along the x-axis) to visualize transcript abundance distributions. Text for each node indicating those regions with scaled transcript abundance >0 is indicated.
Figure 3.
The relationship between cell compartmentalization and morphology.
Panels within this figure correspond to each other, indicating a relationship between morphology, transcript accumulation, and cellular compartments. A) A diagram of Caulerpa morphology. Pseudo-organs roughly correspond to the apical-basal pattern of transcript accumulation shown in neighboring panel B) and the location of transcripts related to cellular compartments as shown in C). B) Heat map for genes belonging to select GO categories showing (left to right) node the parent GO term belongs to, transcript accumulation across pseudo-organs, and the general GO term category. Color indicates scaled transcript abundance, in which average transcript abundance is equal to 0 and variance equal to 1 for each transcript's abundance level across pseudo-organs. Green indicates low and magenta high scaled transcript abundance. C) Diagram of cellular compartments and the flow of genetic information from transcription to translation.
Figure 4.
Recurrent recruitment of transcript accumulation to morphological structures in a land plant and Caulerpa.
A) Intersection of transcript accumulation profiles by their Caulerpa node membership (x-axis) and corresponding accumulation pattern in tomato (Solanum lycopersicum). Each point corresponds to a Caulerpa transcript and its corresponding best BLAST-hit tomato homolog. χ2 p values indicate probability of Caulerpa transcript membership among tomato nodes differing from expected null distribution. Along the side of the graph is indicated averaged scaled transcript abundance across sampled regions in tomato. Intersections of transcript accumulation detailed in C–E are indicated with red boxes. B) Bar graphs showing expected (gray) and observed (yellow, Node 2; red, Node 4; blue, Node 6) distributions of Caulerpa BLAST hits in tomato against tomato nodes. Intersections of transcript accumulation detailed in C–E are indicated. C–E) Line graphs of select intersections of transcripts with similar accumulation profiles in Caulerpa, the homologs of which are enriched for specific transcript accumulation patterns in tomato. Details of gene identities are discussed in the text. Inflor. = inflorescence, Leaf = leaf, Root = root, Sdling = seedling, Stem = stem, Veg = vegetative apex.