Whole-genome resequencing improves the utility of otoliths as a critical
source of DNA for fish stock research and monitoring
Abstract
Fish ear bones, known as otoliths, are often collected by fisheries to
assist in management, and are a common sample type in museum and
national archives. Beyond their utility for aging, morphological and
trace element analysis, otoliths are a repository of valuable genomic
information. Previous work has shown that DNA can be extracted from the
trace quantities of tissue remaining on the surface of otoliths, despite
the fact that they are often stored dry at room temperature. However,
much of this work has used reduced-representation sequencing methods in
clean lab conditions, to achieve adequate yields of DNA, libraries, and
ultimately single-nucleotide polymorphisms (SNPs). Here, we pioneer the
use of small-scale (spike-in) sequencing to screen otolith samples
prepared in regular molecular biology laboratories for contamination and
quality levels, submitting for whole-genome resequencing only samples
above a defined endogenous DNA threshold. Despite the typically low
quality and quantity of DNA extracted from otoliths, we are able to
produce whole-genome libraries and ultimately sets of filtered, unlinked
and even adaptive SNPs of ample size for downstream uses in population,
climate, and conservation genomics. By comparing with a set of tissue
samples from the same species, we are able to highlight the quality and
efficacy of otolith DNA samples from DNA extraction and library
preparation, to bioinformatic preprocessing and SNP calling. We provide
detailed schematics, protocols, and scripts of our approach, such that
it can be adopted widely by the community, improving the use of otoliths
as a source of valuable genomic data.