Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, SE-90187, Umeå, Sweden.
Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, NO-1432, Norway.
Mol Ecol Resour. 2017 Jul;17(4):583-585. doi: 10.1111/1755-0998.12632.
Population genetic studies in nonmodel organisms are often hampered by a lack of reference genomes that are essential for whole-genome resequencing. In the light of this, genotyping methods have been developed to effectively eliminate the need for a reference genome, such as genotyping by sequencing or restriction site-associated DNA sequencing (RAD-seq). However, what remains relatively poorly studied is how accurately these methods capture both average and variation in genetic diversity across an organism's genome. In this issue of Molecular Ecology Resources, Dutoit et al. (2016) use whole-genome resequencing data from the collard flycatcher to assess what factors drive heterogeneity in nucleotide diversity across the genome. Using these data, they then simulate how well different sequencing designs, including RAD sequencing, could capture most of the variation in genetic diversity. They conclude that for evolutionary and conservation-related studies focused on the estimating genomic diversity, researchers should emphasize the number of loci analysed over the number of individuals sequenced.
在非模式生物的群体遗传学研究中，通常缺乏参考基因组，这对于全基因组重测序是至关重要的。有鉴于此，已经开发了基因分型方法来有效地消除对参考基因组的需求，例如测序基因分型或限制位点相关的 DNA 测序（RAD-seq）。然而，这些方法在多大程度上准确地捕捉到整个生物体基因组中遗传多样性的平均值和变化仍然相对研究较少。在本期《分子生态学资源》中，Dutoit 等人（2016 年）使用来自卷叶鹎的全基因组重测序数据来评估是什么因素驱动基因组中核苷酸多样性的异质性。利用这些数据，他们然后模拟不同测序设计（包括 RAD 测序）在多大程度上可以捕获遗传多样性的大部分变化。他们得出的结论是，对于以估计基因组多样性为重点的进化和保护相关研究，研究人员应该强调分析的基因座数量而不是测序的个体数量。
