INRAE, LPGP, Rennes, France.
Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
Mol Ecol Resour. 2021 Jul;21(5):1715-1731. doi: 10.1111/1755-0998.13360. Epub 2021 Mar 9.
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.
非模式物种的性别决定和性染色体组织研究长期以来在技术上具有挑战性，但新的测序方法现在能够精确和高通量地识别性别特异性基因组序列。特别是，限制性位点相关 DNA 测序（RAD-Seq）正在被广泛应用于探索许多植物和动物物种的性别决定系统。然而，缺乏专门用于搜索和可视化 RAD-Seq 数据中性别偏向标记的软件。在这里，我们提出了 RADSex，这是一种计算分析工作流程，旨在使用 RAD-Seq 数据研究性别决定的遗传基础。RADSex 使用简单，所需计算资源很少，对性别决定系统的类型或性染色体结构没有先验假设，并通过专用的 R 包提供方便的可视化。为了演示 RADSex 的功能，我们重新分析了一份已发表的日本青鳉（Oryzias latipes）RAD-Seq 数据集，在该数据集中我们发现了一个以前未知的 Y 染色体多态性。然后，我们使用 RADSex 分析了来自 15 种鱼类的新 RAD-Seq 数据集，这些鱼类跨越了多个分类阶元。我们确定了其中六种物种的性别决定系统和性别特异性标记，其中五种在本研究之前没有已知的性别标记。我们表明，RADSex 由于其分析速度快、资源使用量低、应用和可视化选项简单，极大地促进了非模式物种性别决定系统的研究。此外，我们对来自 15 个物种的新数据集的分析提供了鱼类性别决定的新见解。
