The Coral Symbiomics Lab
Red Sea Research Center
Division of Biological and Environmental Science and Engineering

Lehmann_MolEco_2018

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

​Lehmann, Robert, Damien J. Lightfoot, Celia Schunter, Craig T. Michell, Hajime Ohyanagi, Katsuhiko Mineta, Sylvain Foret, et al. “Finding Nemo’s Genes: A Chromosome-Scale Reference Assembly of the Genome of the Orange Clownfish Amphiprion Percula.” Molecular Ecology Resources 0, no. 0 (September 10, 2018). https://doi.org/10.1111/1755-0998.12939.
Lehmann, Robert, 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
Amphiprion percula, chromosome‐scale assembly, coral reef fish, fish genomics, functionalgenomics, Nemo, orange clownfish
2018
​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.
1755-098X