Exome capture of Antarctic krill (Euphausia superba) for cost effective genotyping and population genetics with historical collections

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 (48Gbp). 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
4,500-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.