Finding Nemo’s Genes: International Team Creates First Reference Genome of Orange Clownfish

The orange clownfish, Amphiprion percula, may have been immortalized in the comedic film “Finding Nemo,” but its importance to the scientific community is no joke.

One of the most important species for studying the ecology and evolution of coral reef fishes, the orange clownfish is also used as a model species to study patterns and processes of social organization, sex change, mutualism, habitat selection, lifespan, and predator-prey interactions. It has been central to ground-breaking research into the scale of larval dispersal and population connectivity in marine fishes.

“Perhaps more than any other species, the orange clownfish has become a mainstay of research into the chemical, molecular, behavioral, population, conservation and climate-change ecology of marine fishes,” says Tim Ravasi, Professor of Bioengineering at the KAUST Environmental Epigenetic Program of King Abdullah University of Science and Technology in Saudi Arabia.

Despite such significance, molecular resources for this species have been scarce and it lacked a reference genome assembly — until now.

Ravisi teamed up with Phil Munday, Reef Research Leader of Coral Reef Ecology at James Cook University in Australia and others to create the first complete assembly of A. percula.

As described in the paper “Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish, Amhiprion percula,” published Sept. 11 in the journal Molecular Ecology Resources, the international team used PacBio Single Molecule, Real-Time (SMRT) Sequencing technology to produce an initial polished assembly comprised of 1,414 contigs, which corresponds to a 121-fold coverage of the genome. Using Hi-C based chromatin contact maps, the genome assembly was placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length.

“This makes it one of the most contiguous and complete fish genome assemblies currently available,” Munday says. “It’s one of those fish that have really been informative for understanding reef biology, which makes it incredibly exciting to have the genome.”

Previous genome assemblies of two other anemonefish, A. frenatus and A. ocellaris, were based on short-read sequencing technology and are too fragmented, the authors state.

“We think that methylation and transposable elements are important for climatization of these reef fishes. In order to study that, you need a chromosome-scale reference,” Munday says. “PacBio is the best technology for generating high-quality genomes.”

Annotated with 26,597 protein coding genes, Munday and Ravasi say the new high-quality assembly, Nemo v1, should be a rich resource for researchers across a wide range of disciplines. Their genomic and transcriptomic data will be available via the Nemo Genome DB database at http://nemogenome.org.

The spiny chromis damselfish, Acanthochromis polyacanthus

Next in their sights are two additional important reef fish species, Spiny chromis damselfish, Acanthochromis polyacanthus, and the Cinnamon clownfish, Amphiprion melanopus. They have also joined the 10K Genome Project, an international effort to sequence the genome of at least one individual from each vertebrate genus, approximately 10,000 genomes.