A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus

• Main Authors: Winter, Sven, de Raad, Jordi, Wolf, Magnus, Coimbra, Raphael T. F., de Jong, Menno J., Schöneberg, Yannis, Christoph, Maria, von Klopotek, Hagen, Bach, Katharina, Pashm Foroush, Behgol, Hanack, Wiebke, Kauffeldt, Aaron Hagen, Milz, Tim, Ngetich, Emmanuel Kipruto, Wenz, Christian, Sonnewald, Moritz, Nilsson, Maria A., Janke, Axel
• Format: Dataset
• Language: unknown
• Published: 2023
• Subjects: Loewe; Omni; Ruan; Hyperoplus lanceolatus
• Online Access: https://zenodo.org/record/7484530; https://doi.org/10.5061/dryad.7pvmcvdxv

Despite increasing sequencing efforts, numerous fish families still lack a reference genome, which complicates genetic research. One such understudied family is the sand lances (Ammodytidae, literally: 'sand burrower'), a globally distributed clade of over 30 fish species that tend to avoid tidal currents by burrowing into the sand. Here, we present the first annotated chromosome-level genome assembly of the great sand eel (Hyperoplus lanceolatus). The genome assembly was generated using Oxford Nanopore Technologies long sequencing reads and Illumina short reads for polishing. The final assembly has a total length of 808.5 Mbp, of which 97.1% were anchored into 24 chromosome-scale scaffolds using proximity-ligation scaffolding. The assembly is highly contiguous with a scaffold and contig N50 of 33.7 Mbp and 31.3 Mbp, respectively, and has a BUSCO completeness score of 96.9%. The presented genome assembly is a valuable resource for future studies of sand lances, as they are of great ecological and commercial importance and may also contribute to studies aiming to resolve the suprafamiliar taxonomy of bony fishes. Funding provided by: LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG)*Crossref Funder Registry ID: Award Number: Genome assembly We assembled the genome of Hyperoplus lanceolatus from Oxford Nanopore (ONT) reads using WTDBG2 v. 2.5 (Ruan & Li, 2019) using the preset for ONT reads (flag '-x ont') followed by three iterations of long-read polishing with racon v.1.4.3 (Vaser et al., 2017), one iteration of polishing with Medaka v.0.11.5 (Oxford Nanopore Technologies LTD., 2018) and three iterations of short-read polishing with pilon v.1.23 (Walker et al., 2014). The assembly was scaffolded into chromosome-scale scaffolds with the Dovetail Genomics´ HiRise pipeline (Putnam et al., 2016) using proximity-ligation data generated by the Dovetail Omni-C kit. Subsequently, gap-closing was performed using TGS-GapCloser v.1.1.1 (Xu et al., 2020), followed by the removal of haplotigs with ...