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

Background

Some of the most widely recognised coral-reef fishes are clownfish or anemonefishes, 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 which 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.

Findings

We generated 43 Gb of short Illumina reads and 9 Gb of long Nanopore reads representing an approximate genome coverage of 54 × and 11 ×, respectively, based on the range of estimated k-mer-predicted genome sizes of between 791 to 967 Mbp. The final assembled genome size is contained in 6,404 scaffolds with an accumulated length of 880 Mb (96.3% BUSCO-calculated genome completeness). Compared to the Illumina-only assembly, the hybrid approach generated 94% fewer scaffolds with 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 reads 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.