A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi-sample genomic data.
A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi-sample genomic data.
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基于多样本基因组数据有效开发高度多态性简单序列重复标记的管道
DOI：
10.1002/ece3.8705
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发表时间：
2022-03
影响因子：
2.6
通讯作者：
Chen D
中科院分区：
文献类型：
--
作者：
Wang H;Gao S;Liu Y;Wang P;Zhang Z;Chen D
即使在基因组学时代，简单序列重复（SSR）也是生态学、进化和保护领域广泛使用的遗传标记，而其应用的普遍限制是开发多态性 SSR 标记的困难。二代测序（NGS）为SSR的快速发展提供了机遇；然而，之前仅使用一个个体的基因组数据开发 SSR 的研究需要冗余实验来测试 SSR 的多态性。在这项研究中，我们设计了一个从多样本基因组数据快速开发多态性 SSR 标记的流程。我们使用生物信息学软件利用重测序数据对多个个体进行基因分型，在实验验证之前检测到高度多态性的SSR，显着提高了效率并减少了实验工作量。该管道已成功应用于全球受威胁的物种——褐马鸡（Crossoptilon mantchuricum），该物种的基因组多样性非常低。新开发的20个SSR标记具有高度多态性，等位基因的平均数量远高于基因组平均数。我们还评估了个体数量和测序深度对SSR挖掘结果的影响，发现10个个体和~10X测序数据足以获得足够数量的多态性SSR，即使对于遗传多样性较低的物种也是如此。此外，如果无法获得高质量基因组，则可以将最佳个体数量和测序深度的 NGS 数据的基因组组装用作替代参考基因组。我们的管道为应用 NGS 技术挖掘和开发生态和进化研究的分子标记提供了范例。我们设计了一个管道，用于从多样本基因组数据快速开发多态性 SSR 标记。该管道已成功应用于全球受威胁的物种——褐尾雉。
Simple sequence repeats (SSRs) are widely used genetic markers in ecology, evolution, and conservation even in the genomics era, while a general limitation to their application is the difficulty of developing polymorphic SSR markers. Next‐generation sequencing (NGS) offers the opportunity for the rapid development of SSRs; however, previous studies developing SSRs using genomic data from only one individual need redundant experiments to test the polymorphisms of SSRs. In this study, we designed a pipeline for the rapid development of polymorphic SSR markers from multi‐sample genomic data. We used bioinformatic software to genotype multiple individuals using resequencing data, detected highly polymorphic SSRs prior to experimental validation, significantly improved the efficiency and reduced the experimental effort. The pipeline was successfully applied to a globally threatened species, the brown eared‐pheasant (Crossoptilon mantchuricum), which showed very low genomic diversity. The 20 newly developed SSR markers were highly polymorphic, the average number of alleles was much higher than the genomic average. We also evaluated the effect of the number of individuals and sequencing depth on the SSR mining results, and we found that 10 individuals and ~10X sequencing data were enough to obtain a sufficient number of polymorphic SSRs, even for species with low genetic diversity. Furthermore, the genome assembly of NGS data from the optimal number of individuals and sequencing depth can be used as an alternative reference genome if a high‐quality genome is not available. Our pipeline provided a paradigm for the application of NGS technology to mining and developing molecular markers for ecological and evolutionary studies. We designed a pipeline for the rapid development of polymorphic SSR markers from multisample genomic data. The pipeline was successfully applied to a globally threatened species, the browneared‐pheasant.
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影响因子：
4.4
作者：
Huang J;Li YZ;Du LM;Yang B;Shen FJ;Zhang HM;Zhang ZH;Zhang XY;Yue BS
通讯作者：
Yue BS
影响因子：
7.7
作者：
Fox, Graeme;Preziosi, Richard F.;Rowntree, Jennifer K.
通讯作者：
Rowntree, Jennifer K.
影响因子：
5.8
作者：
Carvajal-Rodriguez, Antonio
通讯作者：
Carvajal-Rodriguez, Antonio
影响因子：
2.7
作者：
Abdelkrim, Jawad;Robertson, Bruce C.;Gemmell, Neil J.
通讯作者：
Gemmell, Neil J.
影响因子：
3.6
作者：
Hodel RG;Segovia-Salcedo MC;Landis JB;Crowl AA;Sun M;Liu X;Gitzendanner MA;Douglas NA;Germain-Aubrey CC;Chen S;Soltis DE;Soltis PS
通讯作者：
Soltis PS