Abstract
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' syngnatiformes such as seahorses and pipefishes. 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 and 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% 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 27.7%. The chromosome-level assembly of C.lyra provides a high-quality reference genome for future population genomic, phylogenomic, and phylogeographic analyses.
Highlights
The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea
Here, we present the chromosome-level genome assembly of C. lyra
We present the chromosome-level genome of the common dragonet, representing the first genome of the ‘benthic associated’ Syngnathiformes clade as a reference for future population genomic, phylogenomic, and comparative genomic analyses
Summary
The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea. A 100 bp paired-end short-read genomic DNA sequencing library was prepared from the muscle tissue of the female individual. This library was later used for genome assembly polishing. Gene completeness analysis of the long-read based contig assembly (wtdbg2), the Hi-C scaffolded assembly (HiRise), the transcriptome of Callionymus lyra, and the annotation. In addition to the genome, we assembled the transcriptome of C. lyra for subsequent use in the genome annotation using Trinity v.2.9.0 (RRID:SCR_013048) [29, 30] based on the 12.3 Gbp multi-tissue RNAseq data. BUSCO analysis identified 87.0% complete BUSCOs, which suggest a high completeness of the annotation (Figure 2, Table 2)
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