Exome capture of Antarctic krill ( Euphausia superba) for cost effective genotyping and population genetics with historical collections
Abstract Antarctic krill ( Euphausia superba Dana) is a keystone species in the Southern Ocean ecosystem, with ecological and commercial significance. However, its vulnerability to climate change requires an urgent investigation of its adaptive potential to future environmental conditions. Historica...
Published in: | Molecular Ecology Resources |
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Online Access: | http://dx.doi.org/10.1111/1755-0998.14022 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.14022 |
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crwiley:10.1111/1755-0998.14022 2024-09-30T14:25:12+00:00 Exome capture of Antarctic krill ( Euphausia superba) for cost effective genotyping and population genetics with historical collections White, Oliver W. Walkington, Sarah Carter, Hugh Hughes, Lauren Clark, Melody Mock, Thomas Tarling, Geraint A. Clark, Matthew D. 2024 http://dx.doi.org/10.1111/1755-0998.14022 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.14022 en eng Wiley http://creativecommons.org/licenses/by/4.0/ Molecular Ecology Resources ISSN 1755-098X 1755-0998 journal-article 2024 crwiley https://doi.org/10.1111/1755-0998.14022 2024-09-17T04:52:06Z Abstract Antarctic krill ( Euphausia superba Dana) is a keystone species in the Southern Ocean ecosystem, with ecological and commercial significance. However, its vulnerability to climate change requires an urgent investigation of its adaptive potential to future environmental conditions. Historical museum collections of krill from the early 20th century represent an ideal opportunity to investigate how krill have changed over time due to predation, fishing and climate change. However, there is currently no cost‐effective method for implementing population scale collection genomics for krill given its genome size (48 Gbp). Here, we assessed the utility of two inexpensive methods for population genetics using historical krill samples, specifically low‐coverage shotgun sequencing (i.e. ‘genome‐skimming’) and exome capture. Two full‐length transcriptomes were generated and used to identify 166 putative gene targets for exome capture bait design. A total of 20 historical krill samples were sequenced using shotgun and exome capture. Mitochondrial and nuclear ribosomal sequences were assembled from both low‐coverage shotgun and off‐target of exome capture data demonstrating that endogenous DNA sequences could be assembled from historical collections. Although, mitochondrial and ribosomal sequences are variable across individuals from different populations, phylogenetic analysis does not identify any population structure. We find exome capture provides approximately 4500‐fold enrichment of sequencing targeted genes, suggesting this approach can generate the sequencing depth required to call identify a significant number of variants. Unlocking historical collections for genomic analyses using exome capture, will provide valuable insights into past and present biodiversity, resilience and adaptability of krill populations to climate change. Article in Journal/Newspaper Antarc* Antarctic Antarctic Krill Euphausia superba Southern Ocean Wiley Online Library Antarctic Southern Ocean Molecular Ecology Resources |
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Open Polar |
collection |
Wiley Online Library |
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crwiley |
language |
English |
description |
Abstract Antarctic krill ( Euphausia superba Dana) is a keystone species in the Southern Ocean ecosystem, with ecological and commercial significance. However, its vulnerability to climate change requires an urgent investigation of its adaptive potential to future environmental conditions. Historical museum collections of krill from the early 20th century represent an ideal opportunity to investigate how krill have changed over time due to predation, fishing and climate change. However, there is currently no cost‐effective method for implementing population scale collection genomics for krill given its genome size (48 Gbp). Here, we assessed the utility of two inexpensive methods for population genetics using historical krill samples, specifically low‐coverage shotgun sequencing (i.e. ‘genome‐skimming’) and exome capture. Two full‐length transcriptomes were generated and used to identify 166 putative gene targets for exome capture bait design. A total of 20 historical krill samples were sequenced using shotgun and exome capture. Mitochondrial and nuclear ribosomal sequences were assembled from both low‐coverage shotgun and off‐target of exome capture data demonstrating that endogenous DNA sequences could be assembled from historical collections. Although, mitochondrial and ribosomal sequences are variable across individuals from different populations, phylogenetic analysis does not identify any population structure. We find exome capture provides approximately 4500‐fold enrichment of sequencing targeted genes, suggesting this approach can generate the sequencing depth required to call identify a significant number of variants. Unlocking historical collections for genomic analyses using exome capture, will provide valuable insights into past and present biodiversity, resilience and adaptability of krill populations to climate change. |
format |
Article in Journal/Newspaper |
author |
White, Oliver W. Walkington, Sarah Carter, Hugh Hughes, Lauren Clark, Melody Mock, Thomas Tarling, Geraint A. Clark, Matthew D. |
spellingShingle |
White, Oliver W. Walkington, Sarah Carter, Hugh Hughes, Lauren Clark, Melody Mock, Thomas Tarling, Geraint A. Clark, Matthew D. Exome capture of Antarctic krill ( Euphausia superba) for cost effective genotyping and population genetics with historical collections |
author_facet |
White, Oliver W. Walkington, Sarah Carter, Hugh Hughes, Lauren Clark, Melody Mock, Thomas Tarling, Geraint A. Clark, Matthew D. |
author_sort |
White, Oliver W. |
title |
Exome capture of Antarctic krill ( Euphausia superba) for cost effective genotyping and population genetics with historical collections |
title_short |
Exome capture of Antarctic krill ( Euphausia superba) for cost effective genotyping and population genetics with historical collections |
title_full |
Exome capture of Antarctic krill ( Euphausia superba) for cost effective genotyping and population genetics with historical collections |
title_fullStr |
Exome capture of Antarctic krill ( Euphausia superba) for cost effective genotyping and population genetics with historical collections |
title_full_unstemmed |
Exome capture of Antarctic krill ( Euphausia superba) for cost effective genotyping and population genetics with historical collections |
title_sort |
exome capture of antarctic krill ( euphausia superba) for cost effective genotyping and population genetics with historical collections |
publisher |
Wiley |
publishDate |
2024 |
url |
http://dx.doi.org/10.1111/1755-0998.14022 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.14022 |
geographic |
Antarctic Southern Ocean |
geographic_facet |
Antarctic Southern Ocean |
genre |
Antarc* Antarctic Antarctic Krill Euphausia superba Southern Ocean |
genre_facet |
Antarc* Antarctic Antarctic Krill Euphausia superba Southern Ocean |
op_source |
Molecular Ecology Resources ISSN 1755-098X 1755-0998 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1111/1755-0998.14022 |
container_title |
Molecular Ecology Resources |
_version_ |
1811643859614040064 |