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RADSex: a computational workflow to study sex determination using Restriction Site‐Associated DNA Sequencing data

Romain Feron 1, 2, 3, * Qiaowei Pan 1, 3 Ming Wen 1, 4 Boudjema Imarazene 1 Elodie Jouanno 1 Jennifer Anderson 1, 5 Amaury Herpin 1 Laurent Journot 6 Hugues Parrinello 6 Christophe Klopp 7 Verena Kottler 8 Alvaro Roco 8 Kang Du 9, 10 Susanne Kneitz 8 Mateus Adolfi 8 Catherine Wilson 11 Braedan Mccluskey 11 Angel Amores 11 Thomas Desvignes 11 Frederick Goetz 12 Ato Takanashi 13 Mari Kawaguchi 13 H. William Detrich 14 Marcos Oliveira 15 Rafael Nobrega 15 Takashi Sakamoto 16 Masatoshi Nakamoto 16 Anna Wargelius 17 Ørjan Karlsen 17 Zhongwei Wang 8, 18 Matthias Stöck 19 Robert Waterhouse 3, 4 Ingo Braasch 20 John Postlethwait 11 Manfred Schartl 9, 21 Yann Guiguen 1, *
Abstract : The study of sex determination and sex chromosome organisation in non-model species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, Restriction Site-Associated DNA Sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analyzed a published dataset of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyze new RAD-Seq datasets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in non-model species thanks to its speed of analyses, low resource usage, ease of application, and visualization options. Furthermore, our analysis of new datasets from 15 species provides new insights on sex determination in fish.
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https://hal.inrae.fr/hal-03150035
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Submitted on : Tuesday, February 23, 2021 - 2:35:06 PM
Last modification on : Friday, December 3, 2021 - 5:54:09 PM

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Romain Feron, Qiaowei Pan, Ming Wen, Boudjema Imarazene, Elodie Jouanno, et al.. RADSex: a computational workflow to study sex determination using Restriction Site‐Associated DNA Sequencing data. Molecular Ecology Resources, Wiley/Blackwell, 2021, 21 (5), pp.1715-1731. ⟨10.1111/1755-0998.13360⟩. ⟨hal-03150035⟩

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