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

Area of Science:

• Genomics and Bioinformatics
• Evolutionary Biology
• Molecular Genetics

Background:

• Studying sex determination in nonmodel species is challenging due to technical limitations.
• New sequencing technologies like RAD-Seq offer potential for identifying sex-specific genomic sequences.
• A lack of specialized software hinders the analysis and visualization of sex-biased markers from RAD-Seq data.

Purpose of the Study:

• To introduce RADSex, a computational workflow for analyzing RAD-Seq data to study sex determination.
• To provide a user-friendly, resource-efficient tool for identifying sex-specific markers without prior assumptions.
• To facilitate the discovery and visualization of sex determination systems in nonmodel species.

Main Methods:

• Development of RADSex, a computational analysis workflow.
• Application of RADSex to re-analyze existing RAD-Seq data from Japanese medaka (Oryzias latipes).
• Analysis of new RAD-Seq data from 15 diverse fish species.

Main Results:

• RADSex successfully identified a novel Y chromosome polymorphism in Japanese medaka.
• The tool identified sex determination systems and sex-specific markers in six fish species, including five with previously unknown markers.
• RADSex demonstrated efficiency, low resource usage, ease of application, and effective visualization capabilities.

Conclusions:

• RADSex significantly simplifies and accelerates the study of sex determination in nonmodel organisms.
• The workflow enables robust identification of sex-specific markers and systems using RAD-Seq data.
• This study provides new insights into fish sex determination across multiple taxonomic orders.