A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus
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 cu...
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ftpubmed:oai:pubmedcentral.nih.gov:10078159 2023-05-15T16:36:28+02:00 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 2023-01-20 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10078159/ http://www.ncbi.nlm.nih.gov/pubmed/36661278 https://doi.org/10.1093/jhered/esad003 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10078159/ http://www.ncbi.nlm.nih.gov/pubmed/36661278 http://dx.doi.org/10.1093/jhered/esad003 © The American Genetic Association. 2023. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com J Hered Genome Resources Text 2023 ftpubmed https://doi.org/10.1093/jhered/esad003 2023-04-09T01:08:07Z 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. Text Hyperoplus lanceolatus PubMed Central (PMC) Journal of Heredity 114 2 189 194 |
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PubMed Central (PMC) |
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ftpubmed |
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English |
topic |
Genome Resources |
spellingShingle |
Genome Resources 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 |
Genome Resources |
description |
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. |
format |
Text |
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 |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10078159/ http://www.ncbi.nlm.nih.gov/pubmed/36661278 https://doi.org/10.1093/jhered/esad003 |
genre |
Hyperoplus lanceolatus |
genre_facet |
Hyperoplus lanceolatus |
op_source |
J Hered |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10078159/ http://www.ncbi.nlm.nih.gov/pubmed/36661278 http://dx.doi.org/10.1093/jhered/esad003 |
op_rights |
© The American Genetic Association. 2023. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
op_doi |
https://doi.org/10.1093/jhered/esad003 |
container_title |
Journal of Heredity |
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114 |
container_issue |
2 |
container_start_page |
189 |
op_container_end_page |
194 |
_version_ |
1766026805996683264 |