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

doi:10.1007/s12686-023-01331-5

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

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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 and Pierre Feutry

Conservation genetics resources, Vol.16, pp.11-16

03/2024

DOI: https://doi.org/10.1007/s12686-023-01331-5

Appears in Recent Faculty of Science and Engineering Publications

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Abstract

RADseq

ddRAD

DArTseq

SNPs

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.

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Title: An R-based tool for identifying sex-linked markers from restriction site-associated DNA sequencing with applications to elasmobranch conservation
Creators: Floriaan Devloo-Delva - CSIRO
Thierry Gosselin
Paul A. Butcher - Southern Cross University
Peter M. Grewe - CSIRO
Charlie Huveneers - Flinders University
Robin B. Thomson - CSIRO
Jonathan M. Werry - Griffith University
Pierre Feutry - CSIRO
Publication Details: Conservation genetics resources, Vol.16, pp.11-16
Publisher: Springer Dordrecht
Identifiers: 991013157313502368
Academic Unit: Faculty of Science and Engineering
Language: English
Resource Type: Journal article

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

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