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 C. 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)
1
LPGP -
Laboratoire de Physiologie et Génomique des Poissons = Fish Physiology and Genomics Institute
2 SIB - Swiss Institute of Bioinformatics [Lausanne]
3 DEE - Department of Ecology and Evolution [UNIL, Lausanne] = Département d'écologie et évolution
4 State Key Laboratory of Developmental Biology of Freshwater Fish
5 Department of Systematic Biology [Uppsala]
6 IGF - Institut de Génomique Fonctionnelle
7 SIGENAE - Système d'Information des GENomes des Animaux d'Elevage
8 Physiological Chemistry, Biocenter
9 The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry
10 JMU - Julius-Maximilians-Universität Würzburg
11 Institute of Neuroscience, University of Oregon, Eugene, Oregon
12 Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center
13 Department of Materials and Life Sciences
14 Department of Marine and Environmental Sciences, Marine Science Center
15 Department of Structural and Functional Biology
16 Department of Aquatic Marine Biosciences
17 IMR - Institute of Marine Research [Bergen]
18 Institute of Hydrobiology [Wuhan]
19 IGB - Leibniz Institute of Freshwater Ecology and Inland Fisheries
20 Department of Integrative Biology, Michigan State University
21 Developmental Biochemistry, Biocenter
2 SIB - Swiss Institute of Bioinformatics [Lausanne]
3 DEE - Department of Ecology and Evolution [UNIL, Lausanne] = Département d'écologie et évolution
4 State Key Laboratory of Developmental Biology of Freshwater Fish
5 Department of Systematic Biology [Uppsala]
6 IGF - Institut de Génomique Fonctionnelle
7 SIGENAE - Système d'Information des GENomes des Animaux d'Elevage
8 Physiological Chemistry, Biocenter
9 The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry
10 JMU - Julius-Maximilians-Universität Würzburg
11 Institute of Neuroscience, University of Oregon, Eugene, Oregon
12 Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center
13 Department of Materials and Life Sciences
14 Department of Marine and Environmental Sciences, Marine Science Center
15 Department of Structural and Functional Biology
16 Department of Aquatic Marine Biosciences
17 IMR - Institute of Marine Research [Bergen]
18 Institute of Hydrobiology [Wuhan]
19 IGB - Leibniz Institute of Freshwater Ecology and Inland Fisheries
20 Department of Integrative Biology, Michigan State University
21 Developmental Biochemistry, Biocenter
Romain Feron
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- IdHAL : romainferon
- ORCID : 0000-0001-5893-6184
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Elodie Jouanno
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Amaury Herpin
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Laurent Journot
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- IdHAL : ljournot
- ORCID : 0000-0003-3499-8887
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Christophe C. Klopp
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- IdHAL : 0000-0001-7126-5477
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Kang Du
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- ORCID : 0000-0002-1497-8945
Zhongwei Wang
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Matthias Stöck
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- ORCID : 0000-0003-4888-8371
Ingo Braasch
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- ORCID : 0000-0003-4766-611X
John Postlethwait
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- PersonId : 791493
- ORCID : 0000-0002-5476-2137
Manfred Schartl
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- ORCID : 0000-0001-9882-5948
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Yann Guiguen
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- ORCID : 0000-0001-5464-6219
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Résumé
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.