Figure 2
Evolutionary analysis of coral genomes. (a) Predicted secondary structures of two typical SCORs in the M. capitata genome (Methods). These were initially identified in transcriptomic data. The predicted minimum free energy (MFE) secondary structures are shown, with the colors corresponding to base-pairing probabilities (red is more stable). For unpaired regions, the color denotes the probability of being unpaired. Mcap.SCOR.01 is described in the text, whereas Mcap.SCOR02, a 572 bp long repeat has 9,758 copies accounting for 4Mbp of the M. capitata genome. This repeat is found 4,582 times in the intron regions of 4,035 genes, and 5,176 copies are in intergenic regions. These target genes include ras-specific guanine nucleotide-releasing factor, centrosome-associated protein, indole-3-acetaldehyde oxidase, and a G-protein coupled receptor. (b) Example of a M. capitata genome contig showing its complex structure. Genes are in dark green, intron-exon structures are in yellow, and intron and UTR-encoded SCORs are in light green. (c) Location of the bacterium-derived 4-gene cluster in M. capitata genome contig144. The coral (animal) genes and HGT candidates are shown in light brown and dark grey filled boxes, respectively.
