Summary We describe eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences. Availability and implementation eMPRess is freely available at http://www.cs.hmc.edu/empress. Supplementary information Supplementary data are available at Bioinformatics online.

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.

24Background: Over 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range 25 of environments, from shallow tropical seas to the deep-ocean floor. They are important 26 foundation species that create coral "forests" which provide unique niches and three-dimensional 27 living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves 28 in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially 29 interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and 30 produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although 31 several cnidarian genomes are currently available, the majority are from hexacorals. Here, we 32 present a de novo assembly of the R. muelleri genome, making this the first complete draft 33 genome from an octocoral. 34 Findings: We generated a hybrid de novo assembly using the Maryland Super-Read Celera 35 Assembler v.3.2.6 (MaSuRCA). The final assembly included 4,825 scaffolds and a haploid 36 genome size of 172 Mb. A BUSCO assessment found 88% of metazoan orthologs present in the 37 genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had 38 detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or 39 to the Uniprot database. Although the R. muelleri genome is smaller (172 Mb) than other 40 publicly available, hexacoral genomes (256-448 Mb), the R. muelleri genome is similar to the 41 hexacoral genomes in terms of the number of complete metazoan BUSCOs and predicted gene 42 models. 43 Conclusions: The R. muelleri hybrid genome provides a novel resource for researchers to 44 investigate the evolution of genes and gene families within Octocorallia and more widely across 45 3Anthozoa. It will be a key resource for future comparative genomics with other corals and for 46 understanding the genomic basis of coral diversity. 47 48