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Whole-genome resequencing improves the utility of otoliths as a critical source of DNA for fish stock research and monitoring
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  • Jilda Caccavo,
  • Larissa Arantes,
  • Enrique Celemín,
  • Susan Mbedi,
  • Sarah Sparmann,
  • Camila Mazzoni
Jilda Caccavo
Institut Pierre Simon Laplace

Corresponding Author:ergo@jildacaccavo.com

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Larissa Arantes
Universidade Federal de Minas Gerais
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Enrique Celemín
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Susan Mbedi
Berlin Center for Genomics in Biodiversity Research
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Sarah Sparmann
Leibniz-Institute of Freshwater Ecology and Inland Fisheries in the Forschungsverbund Berlin eV
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Camila Mazzoni
Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin eV
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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.
10 Feb 2024Submission Checks Completed
10 Feb 2024Assigned to Editor
10 Feb 2024Review(s) Completed, Editorial Evaluation Pending
19 Feb 2024Submitted to Molecular Ecology Resources
18 Jun 2024Review(s) Completed, Editorial Evaluation Pending
08 Jul 2024Editorial Decision: Revise Minor
21 Jul 20242nd Revision Received
24 Jul 2024Submission Checks Completed
24 Jul 2024Assigned to Editor
24 Jul 2024Review(s) Completed, Editorial Evaluation Pending
15 Aug 2024Editorial Decision: Accept