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

Abstract

BackgroundThe 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.FindingsHere, 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%.ConclusionsThe chromosome-level assembly of C. lyra provides a high-quality reference genome for future population genomic, phylogenomic, and phylogeographic analyses.

Near chromosome-level and highly repetitive genome assembly of the snake pipefishEntelurus aequoreus(Syngnathiformes: Syngnathidae)

“…The data generation and analyses presented here were conducted during a six-week master course in 2021 at the Goethe University, Frankfurt am Main, Germany. The concept of high-quality genome sequencing in a course setting has so far yielded three reference-quality genomes of fish and has proven to be a successful approach to introduce the technology to a new generation of scientists [18][19][20][21].…”