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Cited by 96Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsFish Biology and Ecology Studies

Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish ( Amphiprion ocellaris ) genome assembly

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Tan, Mun Hua, Austin, Christopher M, Hammer, Michael P, Lee, Yin Peng, Croft, Laurence J, Gan, Han Ming·2018·GigaScience
DOI 10.1093/gigascience/gix137PMC PMC5848817
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Abstract

Background: Some of the most widely recognized coral reef fishes are clownfish or anemonefish, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity, and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Moreover, there are some curious geographic-based phenotypes that warrant investigation. Leveraging on the advancement in Nanopore long read technology, we report the first hybrid assembly of the clown anemonefish (Amphiprion ocellaris) genome utilizing Illumina and Nanopore reads, further demonstrating the substantial impact of modest long read sequencing data sets on improving genome assembly statistics. Results: We generated 43 Gb of short Illumina reads and 9 Gb of long Nanopore reads, representing approximate genome coverage of 54× and 11×, respectively, based on the range of estimated k-mer-predicted genome sizes of between 791 and 967 Mbp. The final assembled genome is contained in 6404 scaffolds with an accumulated length of 880 Mb (96.3% BUSCO-calculated genome completeness). Compared with the Illumina-only assembly, the hybrid approach generated 94% fewer scaffolds with an 18-fold increase in N50 length (401 kb) and increased the genome completeness by an additional 16%. A total of 27 240 high-quality protein-coding genes were predicted from the clown anemonefish, 26 211 (96%) of which were annotated functionally with information from either sequence homology or protein signature searches. Conclusions: We present the first genome of any anemonefish and demonstrate the value of low coverage (~11×) long Nanopore read sequencing in improving both genome assembly contiguity and completeness. The near-complete assembly of the A. ocellaris genome will be an invaluable molecular resource for supporting a range of genetic, genomic, and phylogenetic studies specifically for clownfish and more generally for other related fish species of the family Pomacentridae.

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  • Combining short- and long-read sequencing technologies in hybrid assemblies recently produced high-quality genomes in fish.

    “Combining short- and long-read sequencing technologies in hybrid assemblies recently produced high-quality genomes in fish8,9.”

    From Hybrid genome assembly and annotation of Danionella translucida (2019) · cites this paper as [8]

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Authors
Tan, M. H., Austin, C. M., Hammer, M. P., Lee, Y. P., Croft, L. J., & Gan, H. M.
Affiliations
  • Monash University Malaysia (MY)
  • Museum and Art Gallery of the Northern Territory, Darwin 0801, Australia
  • Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
Corresponding author
Gan, Han Ming
ORCID
Venue
GigaScience
Publisher
Oxford University Press (OUP)
Published
2018-01-12
Volume
7
Issue
3
Pages
1-6
ISSN
2047-217X (ISSN-L)
DOI
10.1093/gigascience/gix137
PMC
PMC5848817
OpenAlex
W2784179637
Cited by
96
References
3
Citations by year
2026: 3 · 2025: 5 · 2024: 7 · 2023: 9 · 2022: 12 · 2021: 15 · 2020: 17 · 2019: 20 · 2018: 8
FWCI
5.24
Type
journal article
Language
en
Open access
Licence
Locations
  • GigaScience (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by)
  • Figshare (submittedVersion, cc-by)
Funders
  • Monash University
  • Monash University Malaysia
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Fish Biology and Ecology Studies
Keywords
Amphiprion ocellaris, clownfish, anemonefish, genome assembly, hybrid assembly, Oxford Nanopore long reads, Illumina sequencing, genome completeness, genome contiguity, gene prediction, Pomacentridae, coral reef fish
MeSH terms
Animals, Perciformes, Phylogeny, Genome, Sequence Analysis, DNA, Genomics, Nanopores, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing

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