De novo genome assembly of the Edwardsiid anthozoan Edwardsia elegans

Abstract

Cnidarians (sea anemones, corals, hydroids, and jellyfish) are a key outgroup for comparisons with bilateral animals to trace the evolution of genomic complexity and diversity within the animal kingdom, as they separated from most other animals 100 s of million years ago. Cnidarians have extensive diversity, yet the paucity of genomic resources limits our ability to compare genomic variation between cnidarian clades and species. Here, we report the genome for Edwardsia elegans, a sea anemone in the most specious genus of the family Edwardsiidae, a phylogenetically important family of sea anemones that contains the model anemone Nematostella vectensis. The E. elegans genome is 396 Mb in length and is predicted to encode approximately 49,000 proteins. We annotated a large conservation of macrosynteny between E. elegans and other Edwardsiidae anemones as well as conservation of both microRNAs and ultra-conserved noncoding elements previously reported in other cnidarians species. We also highlight microsyntenic variation of clustered developmental genes and ancient gene clusters that vary between species of sea anemones, despite previous research showing conservation between cnidarians and bilaterians. Overall, our analysis of the E. elegans genome highlights the importance of using multiple species to represent a taxonomic group for genomic comparisons, where genomic variation can be missed for large and diverse clades.

Keywords: Anthozoa; cnidaria; genome sequencing; genomic diversity; microRNA; synteny.

Fig. 1.

a) Edwardsia elegans in the recirculating aquaria at UNC Charlotte. b) Phylogenetic tree with node number representing duplications. c) Snail plot of the E. elegans genome generated using BlobToolKit (Challis et al. 2020). d) Repetitive Regions of the genome.

Fig. 2.

Venn Diagram showing the number of species specific and shared Single-Copy Orthologs found between the three edwardsiid species.

Fig. 3.

Macrosyntenic regions between E. elegans and a) N. vectensis and b) S. callimorphus. Each dot represents the best one-to-one reciprocal BLASTp hit for a protein between the two species. c) A ribbon plot of single-copy orthologs showing macrosynteny between E. elegans and S. callimorphus and N. vectensis.

Fig. 4.

Microsyntenic comparisons between E. elegans and the three other actinarians. a) Hbn–Otp–Rx and an UCNE b) HOX c) wnt5 and 7/7a.

Fig. 5.

Dot plot of UCNE regions between a) E. elegans and S. callimorphus and b) E. elegans and N. vectensis.

Fig. 6.

Annotation of the E. elegans miRNA repertoire. a) Two distinct populations of small-RNA reads: putative siRNAs/miRNAs (19–23nt) and putative piRNAs (27–31nt). b) miRNA sequences exhibit a bias toward uridine at position one. WebLogo3 was utilized to create sequence logos (Crooks et al. 2004). c) The miRNAs that are evolutionarily conserved between E. elegans and other sequenced anthozoan species.