The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into the melanic pigmentation of anemonefish

Moore, Billy, Herrera, Marcela, Gairin, Emma, Li, Chengze, Miura, Saori, Jolly, Jeffrey, Mercader, Manon, Izumiyama, Michael, Kawai, Erina, Ravasi, Timothy, Laudet, Vincent, and Ryu, Taewoo (2023) The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into the melanic pigmentation of anemonefish. G3: Genes, Genomes, Genetics, 13 (3). jkad002.

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Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses 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 of A. clarkii is 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 among 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 of erbb3b (a gene involved in melanocyte development) in A. clarkii compared with other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkii's many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.

Item ID: 78370
Item Type: Article (Research - C1)
ISSN: 2160-1836
Keywords: Amphiprion clarkii, anemonefish, chromosome-scale assembly, erbb3b, genome, melanism, pigmentation
Copyright Information: © The Author(s) 2023. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Research Data:
Date Deposited: 11 Oct 2023 01:40
FoR Codes: 31 BIOLOGICAL SCIENCES > 3103 Ecology > 310305 Marine and estuarine ecology (incl. marine ichthyology) @ 100%
SEO Codes: 18 ENVIRONMENTAL MANAGEMENT > 1805 Marine systems and management > 180504 Marine biodiversity @ 100%
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