The genome of the deep-sea anemone Actinernus sp. contains a mega-array of ANTP-class homeobox genes

Abstract

Members of the phylum Cnidaria include sea anemones, corals and jellyfish, and have successfully colonized both marine and freshwater habitats throughout the world. The 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 sp., which was 1.39 Gbp in length and contained 44 970 gene models including 14 806 tRNA genes and 30 164 protein-coding genes. Analyses of homeobox genes revealed the longest chromosome hosts a mega-array of Hox cluster, HoxL, NK cluster and NKL homeobox genes; until now, such an array has only been hypothesized to have existed in ancient ancestral genomes. In addition to this striking arrangement of homeobox genes, analyses 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. Also, compared with other sea anemones, circadian rhythm genes were lost in Actinernus sp., which likely reflects adaptation to living in the dark. This high-quality genome of a deep-sea cnidarian thus reveals some of the likely molecular adaptations of this ecologically important group of metazoans to the extreme deep-sea environment. It also deepens our understanding of the evolution of genome content and organization of animals in general and cnidarians in particular, specifically from the viewpoint of key developmental control genes like the homeobox-encoding genes, where we find an array of genes that until now has only been hypothesized to have existed in the ancient ancestor that pre-dated both the cnidarians and bilaterians.

Venomics Reveals the Venom Complexity of Sea Anemone Heteractis magnifica

“…To identify potential toxin-like transcripts, the translated transcriptome data were compared with putative animal toxin sequences, which were previously achieved by searching various public databases (with an E-value ≤ 10 −5 as the threshold) [80]. Searches were conducted against five public databases, including (a) the Kyoto Encyclopedia of Genes and Genomes (KEGG) [81,82], (b) cnidarian protein sequences from the Gen-Bank non-redundant (Nr) protein database [83], (c) UniProt animal toxin and venom database (UniProt) [84], (d) clusters of orthologous groups for eukaryotic complete genomes (KOG) [85], and (e) Gene Ontology (GO).…”