Abstract
BackgroundSome 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.ResultsWe 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.ConclusionsWe 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.
Highlights
Some of the most widely recognized coral reef fishes are clownfish or anemonefish, members of the family Pomacentridae
To further contribute to the evaluation of long read technology in fish genomics [15], we sequenced the whole genome of A. ocellaris using Oxford Nanopore and Illumina technologies and demonstrate that hybrid assembly of long and short reads greatly improved the quality of genome assembly
We present the first clownfish genome co-assembled with high-coverage Illumina short reads and low-coverage (∼11×) Nanopore long reads
Summary
Some of the most widely recognized coral reef fishes are clownfish or anemonefish, members of the family Pomacentridae (subfamily: Amphiprioninae). To further contribute to the evaluation of long read technology in fish genomics [15], we sequenced the whole genome of A. ocellaris using Oxford Nanopore and Illumina technologies and demonstrate that hybrid assembly of long and short reads greatly improved the quality of genome assembly. To generate Oxford Nanopore long reads, approximately 5 μg of gDNA was extracted from isolates NTM A4496 and A4497, Figure 1: The clown anemonefish (Amphiprion ocellaris).
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