Finding Nemo's genes: a chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

Lehmann, Robert, Lightfoot, Damien, Schunter, Celia, Michell, Craig T., Ohyanagi, Hajime, Mineta, Katsuhiko, Foret, Sylvain, Berumen, Michael L., Miller, David J., Aranda, Manuel, Gojobori, Takashi, Munday, Philip L., and Ravasi, Timothy (2019) Finding Nemo's genes: a chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula. Molecular Ecology Resources, 19 (3). pp. 570-585.

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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.

Item ID: 58277
Item Type: Article (Research - C1)
ISSN: 1755-0998
Keywords: Amphiprion percula, chromosome-scale assembly, coral reef fish, fish genomics, functional genomics, Nemo, orange clownfish
Copyright Information: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2018 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.
Funders: King Abdullah University of Science and Technology (KAUST)
Projects and Grants: KAUST OCRF-2014-CRG3-62140408
Date Deposited: 15 May 2019 07:39
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060403 Developmental Genetics (incl Sex Determination) @ 100%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960808 Marine Flora, Fauna and Biodiversity @ 100%
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