RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing data

RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing data

The study of sex determination and sex chromosome organization in nonmodel 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 sequencin...

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Bibliographic Details
Published in:Molecular ecology resources Vol. 21; no. 5; pp. 1715 - 1731
Main Authors: Feron, Romain, Pan, Qiaowei, Wen, Ming, Imarazene, Boudjema, Jouanno, Elodie, Anderson, Jennifer, Herpin, Amaury, Journot, Laurent, Parrinello, Hugues, Klopp, Christophe, Kottler, Verena A., Roco, Alvaro S., Du, Kang, Kneitz, Susanne, Adolfi, Mateus, Wilson, Catherine A., McCluskey, Braedan, Amores, Angel, Desvignes, Thomas, Goetz, Frederick W., Takanashi, Ato, Kawaguchi, Mari, Detrich, Harry William, Oliveira, Marcos A., Nóbrega, Rafael H., Sakamoto, Takashi, Nakamoto, Masatoshi, Wargelius, Anna, Karlsen, Ørjan, Wang, Zhongwei, Stöck, Matthias, Waterhouse, Robert M., Braasch, Ingo, Postlethwait, John H., Schartl, Manfred, Guiguen, Yann
Format: Journal Article
Language:English
Published: England Wiley Subscription Services, Inc 01-07-2021
Wiley/Blackwell
Subjects:
Animal species
Chromosomes
computational workflow
Computer applications
Data analysis
Datasets
Deoxyribonucleic acid
DNA
DNA sequencing
Fish
Life Sciences
Markers
Nucleotide sequence
Oryzias latipes
Polymorphism
RAD&#8208
RAD‐Sequencing
Sequencing
Sex
Sex determination
Species
Visualization
Workflow
RAD-Sequencing
computational workflow
visualization
sex determination
fish
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Description
Summary:The study of sex determination and sex chromosome organization in nonmodel 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‐analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD‐Seq data sets 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 nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish.
Bibliography:R.F. designed and implemented RADSEX and SGTR, with feedback from Q.P., M.W. and Y.G., J.H.P., and M.Sch. designed the PhyloSex project and advised on results interpretation. Q.P., M.W., B.I., J.A., A.H., K.K., A.S.R., K.D., S.K., C.K., J.H.P., M.Sch. and Y.G. participated in the analysis of the results. H.P. and L.J. prepared libraries and performed the sequencing. R.F., Q.P., J.H.P., M.Sch. and Y.G. drafted the manuscript. R.F., Q.P., R.M.W., J.H.P., M.Sch. and Y.G. revised the manuscript. Y.G., M.Sch., J.H.P., E.J., S.K., M.W., M.A., C.W., B.M., A.A., T.D., F.W.G., M.K., H.W.D., M.O., R.N., T.S., M.N., M.St., A.W., Ø.K. and I.B. collected, sexed and/or extracted and prepared gDNA samples. All authors approved the final manuscript.
AUTHOR CONTRIBUTIONS
ISSN:1755-098X
1755-0998
1755-0998
DOI:10.1111/1755-0998.13360