A hybrid de novo assembly of the sea pansy ( Renilla muelleri ) genome

  1. Justin B Jiang
  2. Andrea M Quattrini
  3. Warren R Francis
  4. Joseph F Ryan
  5. Estefanía Rodríguez
  6. Catherine S McFadden

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Abstract

Background

More than 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral “forests,” which provide unique niches and 3-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several anthozoan genomes are currently available, the majority of these are hexacorals. Here, we present a de novo assembly of an azooxanthellate shallow-water octocoral, Renilla muelleri.

Findings

We generated a hybrid de novo assembly using MaSuRCA v.3.2.6. The final assembly included 4,825 scaffolds and a haploid genome size of 172 megabases (Mb). A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome may be smaller (172 Mb minimum size) than other publicly available coral genomes (256–448 Mb), the R. muelleri genome is similar to other coral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models.

Conclusions

The R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giz026

    Justin Jiang 1Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Justin JiangAndrea M. Quattrini 1Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andrea M. QuattriniWarren R. Francis 2University of Southern Denmark, Dept. of Biology, Campusvej 55, Odense M 5230, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Warren R. FrancisJoseph F. Ryan 3Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd. St. Augustine, FL 32080, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEstefanía Rodríguez 4Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Estefanía RodríguezCatherine S. McFadden 1Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Catherine S. McFadden

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz026 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101602 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101603

  2. Version published to 10.1093/gigascience/giz026
  3. Version published to 10.1101/424614v1 on bioRxiv