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

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

doi:10.1111/1755-0998.12939

Abstract

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.

Highlights

The orange clownfish, Amphiprion percula, which was immortalized in the film “Finding Nemo,” is arguably the most recognized fish on Earth
The orange clownfish is used as a model species to study patterns and processes of social organization (Buston & Wong, 2014; Buston, Bogdanowicz, Wong, & Harrison, 2007; Wong, Uppaluri, Medina, Seymour, & Buston, 2016), sex change (Buston, 2003), mutualism (Schmiege, D'Aloia, & Buston, 2017), habitat selection (Dixson et al, 2008; Elliott & Mariscal, 2001; Scott & Dixson, 2016), lifespan (Buston & García, 2007) and predator–prey interactions (Dixson, 2012; Manassa, Dixson, McCormick, & Chivers, 2013)
Genomic DNA of an individual orange clownfish (Figure 1a) was sequenced with the Pacific Biosciences (PacBio) RS II platform to generate 1,995,360 long reads, yielding 113.8 Gb, which corresponds to a 121‐fold coverage of the genome (Table S1)

Summary

| INTRODUCTION

The orange clownfish, Amphiprion percula, which was immortalized in the film “Finding Nemo,” is arguably the most recognized fish on Earth. The orange clownfish is one of the relatively few coral reef fishes that can be reared in captivity (Wittenrich, 2007) It has unrivalled potential for experimental manipulation to test ecological and evolutionary questions in marine ecology (Dixson et al, 2014; Manassa et al, 2013), including the impacts of climate change and ocean acidification (Nilsson et al, 2012). The resulting final assembly is highly contiguous with contig and scaffold N50 values of 3.12 and 38.4 Mb, respectively This assembly will be a valuable resource for the research community and will further establish the orange clownfish as a model organism for genetic and genomic studies into ecological, evolutionary and environmental aspects of reef fishes. To facilitate the use of this resource, we have developed an integrated database, the Nemo Genome DB (www.nemogenome.org), which allows for the interrogation and mining of genomic and transcriptomic data described here

| MATERIALS AND METHODS

| RESULTS AND DISCUSSION

| CONCLUSION

DATA ACCESSIBILITY