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 ORCID: https://orcid.org/0000-0001-9604-0362, Tarling, Geraint A. and 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). ISSN 1755-098X

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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.

Item Type:	Article
Additional Information:	Funding Information: This research was funded by the NERC Environmental Omics Facility (NEOF) Early Career Researchers Pilot project competition (NEOF1430) and an Internal Natural History Museum London Science Investment Fund. The NERC Environmental Omics Facility (NEOF) is funded by the UK Natural Environmental Research Council (NERC).
Uncontrolled Keywords:	bioinformatics,exome capture,genome skimming,museomics,biotechnology,ecology, evolution, behavior and systematics,genetics,sdg 13 - climate action ,/dk/atira/pure/subjectarea/asjc/1300/1305
Faculty \ School:	Faculty of Science > School of Environmental Sciences
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	10 Oct 2024 09:30
Last Modified:	13 Nov 2024 00:53
URI:	https://ueaeprints.uea.ac.uk/id/eprint/96977
DOI:	10.1111/1755-0998.14022

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