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Winter S, de Raad J, Wolf M, Coimbra RTF, de Jong MJ, Schöneberg Y, Christoph M, von Klopotek H, Bach K, Foroush BP, Hanack W, Kauffeldt AH, Milz T, Ngetich EK, Wenz C, Sonnewald M, Nilsson MA, Janke A. A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus. J Hered 2023; 114:189-194. [PMID: 36661278 PMCID: PMC10078159 DOI: 10.1093/jhered/esad003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
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. It 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 this family is of great ecological and commercial importance and may also contribute to studies aiming to resolve the suprafamiliar taxonomy of bony fishes.
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Affiliation(s)
- Sven Winter
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany.,Research Institute for Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Jordi de Raad
- Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany.,LOEWE-Centre for Translational Biodiversity Genomics, 60325 Frankfurt am Main, Germany
| | - Magnus Wolf
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany
| | - Raphael T F Coimbra
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany
| | - Menno J de Jong
- Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany
| | - Yannis Schöneberg
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany
| | - Maria Christoph
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany
| | - Hagen von Klopotek
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany
| | - Katharina Bach
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany
| | - Behgol Pashm Foroush
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany
| | - Wiebke Hanack
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany
| | - Aaron Hagen Kauffeldt
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany
| | - Tim Milz
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany
| | - Emmanuel Kipruto Ngetich
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany
| | - Christian Wenz
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany
| | - Moritz Sonnewald
- Senckenberg Research Institute, Department of Marine Zoology, Section Ichthyology, 60325 Frankfurt am Main, Germany
| | - Maria Anna Nilsson
- Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany.,LOEWE-Centre for Translational Biodiversity Genomics, 60325 Frankfurt am Main, Germany
| | - Axel Janke
- Institute for Ecology, Evolution, and Diversity, Goethe University, 60428 Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany.,LOEWE-Centre for Translational Biodiversity Genomics, 60325 Frankfurt am Main, Germany
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