The chromosome-scale genome assembly of the yellowtail clownfishAmphiprion clarkiiprovides insights into melanic pigmentation of anemonefish

Abstract

ABSTRACTAnemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfishAmphiprion clarkiipossesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome ofA. clarkiiis yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0 % of conserved actinopterygian genes, making the quality and completeness of this genome the highest amongst all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers oferbb3b(a gene involved in melanophore development) inA. clarkiicompared to other anemonefish, thus suggesting a possible link betweenerbb3band the natural melanism polymorphism observed inA. clarkii. The publication of this high-quality genome, along withA. clarkii’s many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.