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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, 2 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 10 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 2, 3 Ingo Braasch 20 John Postlethwait 11 Manfred Schartl 9, 10 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 are now enabling 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 designed to specifically search for 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 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 systematic 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 and outperforms the commonly used RAD-Seq analysis software STACKS. RADSex in speed, 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-03048150
Contributor : Maryse Corvaisier <>
Submitted on : Wednesday, December 9, 2020 - 11:02:39 AM
Last modification on : Friday, April 16, 2021 - 3:04:01 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. 2020. ⟨hal-03048150⟩

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