Overview of Hydractinia, phylogenetic analysis, synteny analysis, and analysis of repetitive elements. (A) Hydractinia echinata colony (top); Hydractinia symbiolongicarpus colony (bottom). (B) Maximum likelihood phylogeny estimated from a data set of single-copy orthologs as inferred by OrthoFinder2 showing that the two Hydractinia species cluster together with Clytia hemisphaerica and Hydra vulgaris branching next to them within the Hydrozoa. Divergence times were estimated using the r8s program (Sanderson 2003). The age of Cnidaria was fixed at 570 million years ago (MYA) and the age of Hydrozoa constrained to 500 MYA based upon work by Cartwright and Collins (2007). (C) Syntenic dot plots comparing H. symbiolongicarpus with four cnidarian species: H. echinata, C. hemisphaerica, H. vulgaris, and Nematostella vectensis. Colored boxes indicate linkage groups. (D) Stacked bar chart showing proportions of different transposable element classes in each Hydractinia genome using RepeatMasker de novo analysis. ARTEFACT refers to elements often found in cloning vectors that may contaminate sequencing projects. (E) Repeat landscape analysis showing overall a highly similar evolutionary history of invasion of repetitive elements in the two species. In H. symbiolongicarpus, there was a species-specific recent expansion (at ∼10% nucleotide substitution) of LTR retrotransposons.
