Adaptations to the deep-sea alongside presence of a mega-array of homeobox genes in the genome of the cnidarian Actinernus

Members of the phylum Cnidaria include sea anemones, corals, and
jellyfishes, and have successfully colonised both marine and freshwater
habitats throughout the world. Understanding of how cnidarians adapt to
extreme environments such as the dark, high-pressure deep-sea habitat has
been hindered by the lack of genomic information. Here we report the first
chromosome-level deep-sea cnidarian genome, of the anemone Actinernus.
Analyses of homeobox genes revealed the longest chromosome hosts a
mega-array of Hox cluster, HoxL, ParaHox, NK cluster, and NKL homeobox
genes; until now, such an array has only been hypothesized to have existed
in ancient ancestral genomes. Analysis of microRNAs revealed
cnidarian-specific complements that are distinctive for nested clades of
these animals, presumably reflecting the progressive evolution of the gene
regulatory networks in which they are embedded. Compared to other sea
anemones, circadian rhythm genes were lost in Actinernus, which likely
reflects adaptation to living in the dark. This high-quality genome of a
deep-sea cnidarian deepens our understanding of the evolution of genome
content and organization of animals in general and cnidarians in
particular and reveals some of the molecular adaptations of this
ecologically important group of metazoans to the extreme deep-sea
environment.