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 ORCID: https://orcid.org/0000-0002-3442-3824; Mock, Thomas; Tarling, Geraint A. ORCID: https://orcid.org/0000-0002-3753-5899; Clark, Matthew D.. 2024 Exome capture of Antarctic krill (Euphausia superba) for cost effective genotyping and population genetics with historical collections. Molecular Ecology Resources, 24 (8), e14022. 13, pp. https://doi.org/10.1111/1755-0998.14022

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Text (Open Access) This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium,provided the original work is properly cited. © 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd. Molecular Ecology Resources - 2024 - White - Exome capture of Antarctic krill Euphausia superba for cost effective.pdf - Published Version Available under License Creative Commons Attribution 4.0. Download (1MB) | Preview

Abstract/Summary

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.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	https://doi.org/10.1111/1755-0998.14022
ISSN:	1755-098X
Additional Keywords:	bioinformatics, exome capture, genome skimming, museomics
Date made live:	13 Sep 2024 14:34 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/538024

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