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

Abstract

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

Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes

“…To supplement our comparative analyses with additional syngnathid genomes and a close outgroup we produced linked-reads assemblies for the bluestripe pipefish ( D. excisus ) and the Mandarin dragonet ( S. splendidus ). The D. excisus assembly was used in all subsequent comparative genomic analyses, and the S. splendidus assembly was used in all except the repetitive DNA analyses, in which cases the chromosome-level assembly for a different dragonet, Callionymus lyra was used to maximize completeness ( 22 ). These assemblies were performed using 10× Genomics Chromium technology and the Supernova assembly software ( 23 ), as described in Stervander and Cresko ( 24 ).…”

A highly contiguous nuclear genome assembly of the mandarinfish Synchiropus splendidus (Syngnathiformes: Callionymidae)

“…In addition, the highly contiguous mandarinfish genome assembly will, together with the common dragonet assembly ( Winter et al 2020 ), be an important comparative genomics resource as an outgroup to the highly derived family Syngnathidae, known for its unique vertebrate innovation of male pregnancy, through the brooding of eggs and young in a body pouch. The evolution and the genomic basis of this trait has attracted much recent attention ( Lin et al 2016 ; Small et al 2016 ; Roth et al 2020 ; Zhang et al 2020 ), but other remarkable adaptations include a craniofacial morphology allowing specialized pivot suction feeding through a toothless, tubular mouth; hard body armor; bony spines; prehensile tails; elongated body plan and loss of fins; and camouflage through elaborate appendages ( e.g.…”

“…The clade composed of the aforementioned families makes up order Syngnathiformes (sensu Betancur-R et al 2017 ; Hughes et al 2018 ), in which genome assemblies have been available for suborders Syngnathoidei, Dactylopteroidei, and Mulloidei (sensu Betancur-R et al 2017 ; cf. Figure 2 ), and the first genome assembly for suborder Callionymoidei was only recently published ( Winter et al 2020 ). Whereas several high-quality assemblies within family Syngnathidae, i.e.…”

“…, seahorses, pipefishes, and seadragons have been published in the last few years ( Lin et al 2016 ; Small et al 2016 ; Vertebrate Genomes Project 2019 ; Roth et al 2020 ; Zhang et al 2020 ; Li et al 2021 ), nonsyngnathid syngnathiform species are generally represented by relatively fragmented assemblies (scaffold N50 17–116 Kbp) of low coverage (29–58×; Roth et al 2020 ). An exception with intermediate contiguity and coverage is the striped red mullet Mullus surmuletus (scaffold N50 483 Kbp, 73× coverage; Fietz et al 2020 ), and importantly, the recent chromosome-level genome assembly of the common dragonet Callionymus lyra that was produced by Winter et al (2020) , based on MinION sequencing. The creation of several additional, high-quality reference genomes from across Syngnathiformes is therefore important in general for the genetic analysis of the amazing phenotypic diversity in this clade.…”

A Chromosome-Scale Genome Assembly of the Okapi (Okapia Johnstoni)

“…The development and increasing accessibility of long-read sequencing technologies and long-range scaffolding methods has made chromosome-scale genome assemblies for many animal and plant species possible ( Bickhart et al 2017 ; Marrano et al 2020 ; Winter et al 2020 ; Rhie et al 2021 ), including the okapi’s closest relative, the giraffe ( Farré et al 2019 ; Liu et al 2021 ). The availability of these high-contiguity genomes enables complex comparative genomic studies and the understanding of the genetic factors underpinning unique evolutionary traits, such as hypertension, which is the norm in the exceptionally tall animal ( Liu et al 2021 ).…”