Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

Robert Lehmann, Damien J. Lightfoot, Celia Schunter, Craig T. Michell, Hajime Ohyanagi, Katsuhiko Mineta, Sylvain Foret, Michael L. Berumen, David J. Miller, Manuel Aranda, Takashi Gojobori, Philip L. Munday, Timothy Ravasi

Research output: Contribution to journalArticlepeer-review

35 Scopus citations


The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C-based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein-coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.
Original languageEnglish (US)
Pages (from-to)570-585
Number of pages16
JournalMolecular Ecology Resources
Issue number3
StatePublished - Sep 10 2018

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): OCRF-2014-CRG3-62140408
Acknowledgements: This study was supported by the Competitive Research Funds OCRF-2014-CRG3-62140408 from the King Abdullah University of Science and Technology (KAUST) to T.R., M.L.B. and P.L.M., as well as KAUST baseline support to M.L.B., M.A., T.G. and T.R. This project was completed under JCU Ethics A1233 and A1415. We thank Dr. Jennifer Donelson and staff at JCU's MARFU facility for assistance with animal husbandry, Dr. Susanne Sprungala for DNA extraction for Illumina library preparation, KAUST BCL for the PacBio sequencing, Dr. Hicham Mansour for sequencing advice and Dr. Rita Bartossek for the PacBio library preparations. We thank Dr. Salim Bougouffa for stimulating discussions. We also acknowledge Mr. Tane Sinclair-Taylor for providing the photograph of the orange clownfish (Figure 1a). This paper is dedicated to our good friend and colleague, Dr. Sylvain Foret.


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