Data from: Comparative analysis of convergent jellyfish eyes reveals extensive differences in expression of vision-related genes

Quantifying gene expression across convergent origins of traits clarifies
the degree to which those traits arise from shared versus distinct genetic
programs, revealing how gene re-use relates to the repeatability of
evolution. Eyes are important traits that evolved in many distantly
related lineages, including at least nine times within cnidarians. Here,
we investigate gene expression in eye-bearing and non-visual tissues from
three cnidarian species representing long-diverged lineages where eyes
evolved convergently (Cubozoa, Scyphozoa, and Hydrozoa). We find gene
expression in eye-bearing tissues to be mostly lineage-specific, with only
a small proportion of genes having convergent expression across species.
Nevertheless, all species express homologs of deeply conserved
vision-related genes known from Bilateria, which likely reflects deep
homology (parallel evolution across vast phylogenetic distances) of a
metazoan phototransduction toolkit. A gene tree analysis of opsins—the
prototypical animal photosensors—shows that convergent eyes recruited
different opsin paralogs, with the potential exception of an opsin
ortholog shared between scyphozoan and cubozoan eyes. Our results suggest
that eyes have mostly lineage-specific patterns of gene expression, yet
some key phototransduction components are repeatedly recruited across
multiple independent eye origins in Medusozoa.