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

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.

Genome of an iconic Australian bird: Chromosome-scale assembly and linkage map of the superb fairy-wren (Malurus cyaneus)

“…As with many of the existing chromosome-scale bird assemblies, not all of the microchromosomes are fully resolved and may still benefit from physical mapping methods such as HiC or BioNano optical mapping (Dudchenko et al, 2017;Jiao et al, 2017;Lehmann et al, 2018). A larger sampling of the pedigree would also provide more informative meioses.…”

The rising tide of high‐quality genomic resources

“…Now, clownfish have yet another reason to be in the spotlight. In this issue, Lehmann et al () present a chromosome‐level genome assembly for A. percula with 908.8 Megabases (Mb) of the assembled sequence placed into 24 chromosomes. The A. percula genome is the third, and most contiguous, in a flurry of clownfish genomes published in 2018 (see also Amphiprion frenatus, Marcionetti, Rossier, Bertrand, Litsios, & Salamin, ; Amphiprion ocellaris, Tan et al, ).…”

“…With a scaffold N50 of 38.4 Mb and 98% of the assembly in chromosomal scaffolds, the A. percula genome is one of the most contiguous fish genomes published thus far, surpassing the high water marks of many model fishes that preceded it. Notably absent from the efforts of Lehmann et al (), however, was the need for a large‐scale consortium effort or an assembly approach that required unusually outsized financial resources. Instead, Lehmann et al () took advantage of a confluence of maturing technologies: long‐read sequencing, dedicated assembly algorithms, and proximity‐based techniques for orienting genomic regions into chromosome‐scale groupings.…”

“…Notably absent from the efforts of Lehmann et al (), however, was the need for a large‐scale consortium effort or an assembly approach that required unusually outsized financial resources. Instead, Lehmann et al () took advantage of a confluence of maturing technologies: long‐read sequencing, dedicated assembly algorithms, and proximity‐based techniques for orienting genomic regions into chromosome‐scale groupings. The absence of a sequencing consortium highlights a sea change in genome biology.…”

“…(Both genomes have been cited more than 900 times according to Google Scholar.) Of the 27 published chromosome‐level fish genomes, the A. percula genome stands alone with ~98% of the assembled genome ordered into chromosomes (Figure b, Lehmann et al, ). This impressive feat highlights the power of modern genome sequencing and assembly tools when paired with appropriate resources for the task, a thoughtful approach, and a bit of genomic luck (e.g., few difficult to assemble regions).…”