Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra

Background The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea. All three species show strong sexual dimorphism. The males show strong morphological differentiation, e.g., species-specific colouration and size relations, while the females of different species have few distinguishing characters. Callionymus belongs to the ‘benthic associated clade’ of the order Syngnathiformes. The ‘benthic associated clade’ so far is not represented by genome data and serves as an important outgroup to understand the morphological transformation in ‘long-snouted’ syngnatiforms such as seahorses and pipefishes.

Findings Here, we present the chromosome-level genome assembly of C. lyra. We applied Oxford Nanopore Technologies’ long-read sequencing, short-read DNBseq, and proximity-ligation-based scaffolding to generate a high-quality genome assembly. The resulting assembly has a contig N50 of 2.2 Mbp, a scaffold N50 of 26.7 Mbp. The total assembly length is 568.7 Mbp, of which over 538 Mbp were scaffolded into 19 chromosome-length scaffolds. The identification of 94.5% of complete BUSCO genes indicates high assembly completeness. Additionally, we sequenced and assembled a multi-tissue transcriptome with a total length of 255.5 Mbp that was used to aid the annotation of the genome assembly. The annotation resulted in 19,849 annotated transcripts and identified a repeat content of 27.66%.

Conclusions The chromosome-level assembly of C. lyra provides a high-quality reference genome for future population genomic, phylogenomic, and phylogeographic analyses.

Authors: Sven Winter, Stefan Prost, Jordi de Raad, Raphael T. F. Coimbra, Magnus Wolf, Marcel Nebenführ, Annika Held, Melina Kurzawe, Ramona Papapostolou, Jade Tessien, Julian Bludau, Andreas Kelch, Sarah Gronefeld, Yannis Schöneberg, Christian Zeitz, Konstantin Zapf, David Prochotta, Maximilian Murphy, Monica M. Sheffer, Moritz Sonnewald, Maria A. Nilsson, Axel Janke