A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus
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...
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Oxford University Press (OUP)
2023
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Online Access: | http://dx.doi.org/10.1093/jhered/esad003 https://academic.oup.com/jhered/advance-article-pdf/doi/10.1093/jhered/esad003/49319082/esad003.pdf https://academic.oup.com/jhered/article-pdf/114/2/189/49784466/esad003.pdf |
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croxfordunivpr:10.1093/jhered/esad003 2024-05-12T08:04:59+00:00 A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus 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 Anna Janke, Axel Suh, Alexander Centre for Translational Biodiversity Genomics Hesse’s Ministry of Higher Education, Research, and the Arts 2023 http://dx.doi.org/10.1093/jhered/esad003 https://academic.oup.com/jhered/advance-article-pdf/doi/10.1093/jhered/esad003/49319082/esad003.pdf https://academic.oup.com/jhered/article-pdf/114/2/189/49784466/esad003.pdf en eng Oxford University Press (OUP) https://creativecommons.org/licenses/by-nc/4.0/ Journal of Heredity volume 114, issue 2, page 189-194 ISSN 0022-1503 1465-7333 Genetics (clinical) Genetics Molecular Biology Biotechnology journal-article 2023 croxfordunivpr https://doi.org/10.1093/jhered/esad003 2024-04-18T08:14:48Z 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 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. Article in Journal/Newspaper Hyperoplus lanceolatus Oxford University Press Journal of Heredity |
institution |
Open Polar |
collection |
Oxford University Press |
op_collection_id |
croxfordunivpr |
language |
English |
topic |
Genetics (clinical) Genetics Molecular Biology Biotechnology |
spellingShingle |
Genetics (clinical) Genetics Molecular Biology Biotechnology 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 Anna Janke, Axel A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus |
topic_facet |
Genetics (clinical) Genetics Molecular Biology Biotechnology |
description |
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 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. |
author2 |
Suh, Alexander Centre for Translational Biodiversity Genomics Hesse’s Ministry of Higher Education, Research, and the Arts |
format |
Article in Journal/Newspaper |
author |
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 Anna Janke, Axel |
author_facet |
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 Anna Janke, Axel |
author_sort |
Winter, Sven |
title |
A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus |
title_short |
A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus |
title_full |
A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus |
title_fullStr |
A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus |
title_full_unstemmed |
A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus |
title_sort |
chromosome-scale reference genome assembly of the great sand eel, hyperoplus lanceolatus |
publisher |
Oxford University Press (OUP) |
publishDate |
2023 |
url |
http://dx.doi.org/10.1093/jhered/esad003 https://academic.oup.com/jhered/advance-article-pdf/doi/10.1093/jhered/esad003/49319082/esad003.pdf https://academic.oup.com/jhered/article-pdf/114/2/189/49784466/esad003.pdf |
genre |
Hyperoplus lanceolatus |
genre_facet |
Hyperoplus lanceolatus |
op_source |
Journal of Heredity volume 114, issue 2, page 189-194 ISSN 0022-1503 1465-7333 |
op_rights |
https://creativecommons.org/licenses/by-nc/4.0/ |
op_doi |
https://doi.org/10.1093/jhered/esad003 |
container_title |
Journal of Heredity |
_version_ |
1798847244544245760 |