Fig. 2.

Genomic rearrangements in Aiptasia. (A) Correlation between a period of speciation and a period of high TE activity. (Top) Approximate times of divergence of Aiptasia from the anemone species S. elegans, V. paguri, and Bartholomea annulata based on Nei–Gojobori synonymous substitution rates in the COX3 gene (SI Appendix, SI Materials and Methods), which correspond to the Jukes–Cantor distances used to estimate the times of past TE activity. Aiptasia and B. annulata are symbiotic with dinoflagellates; V. paguri and S. elegans are not. (Bottom) The dynamics of seven distinct TE classes, plotted as the cumulative percentage of the genome covered by each class (ordinate) at given Jukes–Cantor substitution distances [abscissa; calculated based on the nucleotide differences between the individual genomic TEs and the consensus sequence for the corresponding TE family (SI Appendix, SI Materials and Methods)]. (B) Arrangements of HOX gene clusters in three anthozoans. N. vectensis and A. digitifera genes are named as described previously (15); Aiptasia genes are named based on the sequence similarities as shown in SI Appendix, Fig. S3C. Arrows indicate directions of transcription. Blue, other homeobox genes; green, HOX and HOX-related genes.