Exploration of Genetic Variations through Single-cell Whole-genome Sequencing in the Model Ciliate Tetrahymena thermophila
Exploration of Genetic Variations through Single-cell Whole-genome Sequencing in the Model Ciliate Tetrahymena thermophila
复制标题
通过单细胞全基因组测序探索纤毛虫嗜热四膜虫模型的遗传变异
DOI：
10.1111/jeu.12746
复制
发表时间：
2019-06-30
影响因子：
2.2
通讯作者：
Miao，Wei
中科院分区：
文献类型：
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作者：
Chen，Kai;Wang，Guangying;Miao，Wei
纤毛虫是单细胞真核生物，具有独立的生殖细胞和体细胞基因组以及不同的生活史，这使得它们成为通过检测遗传变异来提高我们对群体遗传学理解的独特模式。然而，传统的测序方法不能直接应用于纤毛虫，因为大多数是未培养的。单细胞全基因组测序（WGS）是研究微生物遗传变异的有力工具，但尚未在纤毛虫中进行研究。我们比较了使用单细胞WGS和批量DNA WGS来检测模型纤毛四膜虫嗜热四膜虫中的遗传变异，特别是单核苷酸多态性（SNP）。我们的分析表明，（i）单细胞WGS在作图率和基因组覆盖率方面具有优异的性能，但由于扩增偏倚，与批量DNA WGS相比，测序均匀性较低（ii）通过单细胞WGS检测到的假阳性SNP位点倾向于出现在具有特别高的测序深度和高C：G至T：A碱基变化率的基因组区域中;（iii）在三个或更多个细胞中检测到的SNP应该是可靠的（对于来自三个细胞的组合数据，获得83.4-97.4%的检测效率）。该分析方法可用于其它纤毛虫的遗传变异分析，并可拓宽纤毛虫种群遗传学的研究领域。
Ciliates are unicellular eukaryotes with separate germline and somatic genomes and diverse life cycles, which make them a unique model to improve our understanding of population genetics through the detection of genetic variations. However, traditional sequencing methods cannot be directly applied to ciliates because the majority are uncultivated. Single‐cell whole‐genome sequencing (WGS) is a powerful tool for studying genetic variation in microbes, but no studies have been performed in ciliates. We compared the use of single‐cell WGS and bulk DNA WGS to detect genetic variation, specifically single nucleotide polymorphisms (SNPs), in the model ciliateTetrahymena thermophila. Our analyses showed that (i) single‐cell WGS has excellent performance regarding mapping rate and genome coverage but lower sequencing uniformity compared with bulk DNA WGS due to amplification bias (which was reproducible); (ii) false‐positive SNP sites detected by single‐cell WGS tend to occur in genomic regions with particularly high sequencing depth and high rate of C:G to T:A base changes; (iii) SNPs detected in three or more cells should be reliable (an detection efficiency of 83.4–97.4% was obtained for combined data from three cells). This analytical method could be adapted to measure genetic variation in other ciliates and broaden research into ciliate population genetics.