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.
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DOI：
10.1111/1755-0998.13360
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发表时间：
2021-07
影响因子：
7.7
通讯作者：
Guiguen Y
中科院分区：
文献类型：
--
作者：
Feron R;Pan Q;Wen M;Imarazene B;Jouanno E;Anderson J;Herpin A;Journot L;Parrinello H;Klopp C;Kottler VA;Roco AS;Du K;Kneitz S;Adolfi M;Wilson CA;McCluskey B;Amores A;Desvignes T;Goetz FW;Takanashi A;Kawaguchi M;Detrich HW 3rd;Oliveira MA;Nóbrega RH;Sakamoto T;Nakamoto M;Wargelius A;Karlsen Ø;Wang Z;Stöck M;Waterhouse RM;Braasch I;Postlethwait JH;Schartl M;Guiguen Y
非模式物种的性别决定和性染色体组织的研究长期以来在技术上具有挑战性，但新的测序方法现在可以精确和高通量地鉴定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）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，缺乏专门设计用于使用RAD-Seq数据搜索和可视化性别偏见标记的软件。在这里，我们提出了RADSex，一个计算分析工作流程，旨在使用RAD-Seq数据研究性别决定的遗传基础。RADSex使用简单，需要很少的计算资源，不需要事先假设性别决定系统的类型或性别位点的结构，并通过专用的R软件包提供方便的可视化。为了证明RADSex的功能，我们重新分析了日本青鳉的已发表数据集，在那里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种鱼类的新的RAD-Seq数据集，这些鱼类跨越了多个分类目。我们确定了性别决定系统和性别特异性标记在这些物种中，其中五个没有已知的性别标记之前，这项研究。我们表明，RADSex极大地促进了性别决定系统的研究，在非模式物种由于其分析速度，低资源使用，易于应用和可视化选项。此外，我们对来自15个物种的新数据集的分析为鱼类的性别决定提供了新的见解。
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.
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DOI：
10.1098/rstb.2000.0717
发表时间：
2000-11-29
影响因子：
6.3
作者：
Charlesworth, B;Charlesworth, D
通讯作者：
Charlesworth, D
影响因子：
3.1
作者：
Gamble, Tony;McKenna, Erin;Higham, Timothy E.
通讯作者：
Higham, Timothy E.
影响因子：
7
作者：
Corcoran, Padraic;Anderson, Jennifer L.;Johannesson, Hanna
通讯作者：
Johannesson, Hanna
影响因子：
2
作者：
da Silva, Maelin;Matoso, Daniele Aparecida;Feldberg, Eliana
通讯作者：
Feldberg, Eliana
影响因子：
4.9
作者：
Benestan, Laura;Moore, Jean-Sebastien;Bernatchez, Louis
通讯作者：
Bernatchez, Louis