ArticleGigaScience2018
Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- The Complete Chromosome-Level Genome and Mitogenome Assembly ofEcology and evolution · 2026Article
- De novo chromosome-level genome assembly and annotation of the Muscovy duck (Cairina moschata).Poultry science · 2026Article
- ANASFV: a workflow for African swine fever virus whole-genome analysis.Microbial genomics · 2025Article
- The draft genome assembly of the cosmopolitan pelagic fish dolphinfish Coryphaena hippurus.G3 (Bethesda, Md.) · 2025Article
- Convergent gene losses and pseudogenizations in multiple lineages of stomachless fishes.Communications biology · 2024Article
- Convergent genomic signatures associated with vertebrate viviparity.BMC biology · 2024Article
- Genomic resources for the Yellowfin tuna Thunnus albacares.Molecular biology reports · 2024Article
- Whole genome assembly and annotation of the King Angelfish (GigaByte (Hong Kong, China) · 2024Article
- The genome of the sapphire damselfishGigaByte (Hong Kong, China) · 2024Article
- De novo genome assembly and comparative genomics for the colonial ascidian Botrylloides violaceus.G3 (Bethesda, Md.) · 2023Article
- From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).Briefings in bioinformatics · 2023Article
- Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus.G3 (Bethesda, Md.) · 2023Article
- The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into the melanic pigmentation of anemonefish.G3 (Bethesda, Md.) · 2023Article
- Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus).G3 (Bethesda, Md.) · 2023Article
- Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil.Frontiers in plant science · 2023Review
- Anemonefishes: A model system for evolutionary genomics.F1000Research · 2023Review
- Transcriptome Profiling and Expression Localization of Key Sex-Related Genes in a Socially-Controlled Hermaphroditic Clownfish,International journal of molecular sciences · 2022Article
- Sequencing Bait: Nuclear and Mitogenome Assembly of an Abundant Coastal Tropical and Subtropical Fish, Atherinomorus stipes.Genome biology and evolution · 2022Article
- Article
- A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris.G3 (Bethesda, Md.) · 2022Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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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