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首页> 外文期刊>Mycologia >Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor and evaluating whether a reference genome is necessary to assess homology
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Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor and evaluating whether a reference genome is necessary to assess homology

机译：检查通过测序的基因分型技术对蘑菇双色拉卡里亚虫的种群遗传分析的功效，并评估是否需要参考基因组来评估同源性

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Given the diversity and ecological importance of Fungi, there is a lack of population genetic research on these organisms. The reason for this can be explained in part by their cryptic nature and difficulty in identifying genets. In addition the difficulty (relative to plants and animals) in developing molecular markers for fungal population genetics contributes to the lack of research in this area. This study examines the ability of restriction-site associated DNA (RAD) sequencing to generate SNPs in Laccaria bicolor. Eighteen samples of morphologically identified L. bicolor from the United States and Europe were selected for this project. The RAD sequencing method produced anywhere from 290 000 to more than 3 000 000 reads. Mapping these reads to the genome of L. bicolor resulted in 84 000-940 000 unique reads from individual samples. Results indicate that incorporation of non-L. bicolor taxa into the analysis resulted in a precipitous drop in shared loci among samples, suggests the potential of these methods to identify cryptic species. F-statistics were easily calculated, although an observable "noise" was detected when using the "All Loci" treatment versus filtering loci to those present in at least 50% of the individuals. The data were analyzed with tests of Hardy-Weinburg equilibrium, population genetic statistics (F-IS and F-ST), and population structure analysis using the program Structure. The results provide encouraging feedback regarding the potential utility of these methods and their data for population genetic analysis. We were unable to draw conclusions of life history of L. bicolor populations from this dataset, given the small sample size. The results of this study indicate the potential of these methods to address population genetics and general life history questions in the Agaricales. Further research is necessary to explore the specific application of these methods in the Agaricales or other fungal groups.
机译：考虑到真菌的多样性和生态重要性，因此缺乏对这些生物的种群遗传学研究。造成这种现象的部分原因可能是它们的神秘性和鉴定种系的难度。另外，为真菌种群遗传学开发分子标记的困难（相对于动植物）也导致该领域缺乏研究。这项研究检查了限制性位点相关DNA（RAD）测序在双色拉各斯中生成SNP的能力。该项目选择了18个来自美国和欧洲的经形态鉴定的双色乳杆菌样品。 RAD测序方法可产生290,000次至超过3,000,000次读数。将这些读物映射到双色乳杆菌的基因组可从单个样品中获得84 000-940 000个独特读物。结果表明掺入非L。双色分类单元进入分析导致样品之间共享位点的急剧下降，表明这些方法可用于鉴定隐性物种。 F统计量易于计算，尽管使用“所有基因座”处理与过滤至少50％个体中存在的基因座时检测到可观察到的“噪音”。使用Hardy-Weinburg平衡测试，人口遗传统计（F-IS和F-ST）以及使用结构程序对人口结构进行分析，对数据进行了分析。结果提供了令人鼓舞的反馈，关于这些方法的潜在用途及其用于群体遗传分析的数据。鉴于样本量很小，我们无法从该数据集中得出双色乳杆菌种群生活史的结论。这项研究的结果表明，这些方法具有解决Agaricales中种群遗传学和一般生活史问题的潜力。有必要进行进一步的研究以探索这些方法在琼脂或其他真菌类中的具体应用。

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