PDF(Pubmed)
Abstract：
Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi.
摘要：
识别真正的多态变异是序列数据分析中的一个重大挑战，尽管在序列数据中检测低频变异对于估计人口统计学参数和调查遗传过程至关重要，比如选择，在人口内。丛枝菌根（AM）真菌是多核生物，其中单个细胞核作为一个群体集体运作，而跨细胞核的遗传变异程度长期以来一直是科学关注的领域。在这项研究中,我们通过比较AM真菌模型物种的两个不同基因组序列数据集中的多态性发现，研究了多态性发现的模式和替代等位基因频率分布。红藻菌株DAOM197198。本研究中使用的2个数据集是公开可用的，是从合并的孢子和菌丝或从单个孢子扩增的单个核产生的。我们还估计了DAOM197198菌株内的生物体内变化。我们的结果表明，这2个数据集对发现的变体表现出不同的频率模式。整个有机体的数据集显示了一个跨越低，中介-，和高频变体，而单核数据集主要以低频变异为特征，在中频和高频中比例较小。此外，整个生物体和单个细胞核内的单核苷酸多态性密度估计证实了DAOM197198菌株的低生物体内变异，并且大多数变体很少见。我们的研究强调了与在AM真菌全基因组序列数据中检测低频变异相关的方法学挑战，并证明了可以在AM真菌的单个核中可靠地鉴定出替代等位基因。
