修剪树:比较OTUs和ASVs在5S-IGS核核核糖体DNA的高通量测序在植物遗传学研究中
Simone Cardoni1, Roberta Piredda2,3, Guido W Grimm4
1Water Research Institute (IRSA), National Research Council Taranto Italy.
Ecology and evolution
|October 9, 2025
概括
使用5SRNA基因测序来划分物种进化是复杂的. 由DADA2识别的扩展序列变异 (ASV) 比MOTHUR的操作分类单元 (OTU) 更有效,简化了数据管理和遗传学分析.
科学领域:
- 基因组学和生物信息学
- 分子进化分子进化
- 植物分类学 植物分类学
背景情况:
- 核核糖体5SRNA基因组为基因分类学和进化研究具有价值.
- 高吞吐量测序产生了难以管理的大数据集,往往导致冗余和错误.
- 在下游分析中,有效减少数据而不会丢失遗传信号至关重要.
研究的目的:
- 为了比较操作分类单元 (OTU) 和片序列变异 (ASV) 在分析5S跨基因间隔器 (5S-IGS) 片的性能.
- 评估两个流行的生物信息学工具,MOTHUR和DADA2,它们在数据处理和基因推理方面的有效性.
- 评估不同数据处理方法的能力,以捕获诊断5S-IGS变体并反映Fagus物种的进化模式.
主要方法:
- 从7种*Fagus*物种的5S-IGS安普利康中生成的OTU (100%相同性) 和ASV的比较分析.
- 使用MOTHUR和DADA2生物信息管道进行序列数据处理.
- 评估了定量指标 (序列计数,共享/独一无二的序列) 和定性指标 (多样性,数据坚固性,基因组合一致性).
主要成果:
- 超过70%的处理读数在OTU和ASV数据集之间共享.
- 尽管代表性序列减少了>80%,但DADA2-ASV在*Fagus*中确定了所有主要的5S-IGS变异,准确地反映了家族遗传和多样性模式.
- MOTHUR产生了较高比例的罕见OTU/ASV,复杂化了遗传学推断,并引入了冗余性.
结论:
- 生物信息学管道选择 (DADA2与MOTHUR) 对5S-IGS数据中检测到的序列变异和家族遗传信息内容的影响最小.
- 在5S-IGS研究中,DADA2-ASV为OTU提供了更有效,更高效的计算替代方案.
- 建议对DADA2-ASV进行复杂进化现象的未来研究,如杂交和多化,特别是在大型样本组中.
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