RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data.
RAD-Sequencing
computational workflow
fish
sex determination
visualization
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Jul 2021
Jul 2021
Historique:
revised:
09
02
2021
received:
31
05
2020
accepted:
11
02
2021
pubmed:
17
2
2021
medline:
20
8
2021
entrez:
16
2
2021
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 33590960
doi: 10.1111/1755-0998.13360
pmc: PMC8589568
mid: NIHMS1750032
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1715-1731Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM139635
Pays : United States
Organisme : National Science Foundation (USA) Office of Polar Programs
ID : PLR-1444167
Organisme : Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
ID : PP00P3_170664
Organisme : NIGMS NIH HHS
ID : R01 GM085318
Pays : United States
Organisme : National Institute of Health (USA)
ID : R01GM085318
Organisme : Agence Nationale de la Recherche
ID : SCHA 408/10-1
Organisme : National Institute of Health (USA)
ID : R35GM139635
Organisme : National Science Foundation (USA) Office of Polar Programs
ID : PLR-1247510
Organisme : Agence Nationale de la Recherche
ID : ANR-10-INBS-09
Organisme : National Science Foundation (USA) Office of Polar Programs
ID : OPP-1543383
Organisme : Deutsche Forschungsgemeinschaft
ID : SCHA 408/10-1
Informations de copyright
© 2021 John Wiley & Sons Ltd.
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