A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome. Issue 4 (3rd April 2019)

• Record Type: Journal Article
• Authors: Jiang, Justin B; Quattrini, Andrea M; Francis, Warren R; Ryan, Joseph F; Rodríguez, Estefanía; McFadden, Catherine S
• Is Part Of: GigaScience. Volume 8:Issue 4(2019)
• Publication Date: 2019-04-03
• Subjects: octocoral -- hybrid assembly -- gene prediction -- Augustus -- PacBio -- MaSuRCA; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giz026
• Languages: English
• ISSNs: 2047-217X

Abstract

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.