An R-based tool for identifying sex-linked markers from restriction site-associated DNA sequencing with applications to elasmobranch conservation

Floriaan Devloo-Delva, Thierry Gosselin, Paul A. Butcher, Peter M. Grewe, Charlie Huveneers, Robin B. Thomson, Jonathan M. Werry, Pierre Feutry

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Abstract

Identifying sex-linked markers from genomic data has both theoretical and applied importance, especially in conservation. Yet, few methods and tools exist to detect such markers from Restriction-site-Associated DNA sequencing reads and even fewer tools can identify sex-linked markers from existing genotyped data. Here, we describe a new R function that can identify sex-linked markers in species with partially non-recombining sex chromosomes. We test the accuracy and speed of our function with an example dataset from a species of conservation concern, the White Shark, Carcharodon carcharias. We further compare our method against other approaches and find that our method detects more sex-linked markers that can be reliably mapped to reference genomes. Overall, we provide a conservation and fisheries-relevant tool that can reliably and efficiently assign sex from genetic data in species with a heterogametic sex and we demonstrate its utility by developing a sex-identification PCR test for White Sharks.

Original languageEnglish
Pages (from-to)11-16
Number of pages6
JournalConservation Genetics Resources
Volume16
Issue number1
Early online date16 Nov 2023
DOIs
Publication statusPublished - Mar 2024

Keywords

  • DArTseq
  • ddRAD
  • RADseq
  • SNPs

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