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对于纳米孔元编码,什么质量足够? 重新考虑方法和Ectomycorrhizae在腐烂中的Fagus sylvatica树皮作为案例研究

Glen Dierickx^1,2, Lowie Tondeleir¹, Pieter Asselman¹

¹Research Group Mycology, Ghent University, 9000 Gent, Belgium.

Journal of fungi (Basel, Switzerland)

|October 25, 2024

概括

纳米孔测序提供可靠的真菌metabarcoding与新的质量过指南. 严格的映射和UNITE物种假设系统提高了真菌群体分析的可复制性.

科学领域:

菌类学菌类学是指菌类学.
生物信息学是一种生物信息学.
生态生态学生态生态学

背景情况:

纳米孔测序技术已经实现了高原始读取精度 (>99%),为metabarcoding应用提供了机会.
标准化质量过协议对于使用纳米孔数据的真菌metabarcoding中可靠的分类学单元恢复至关重要.

研究的目的:

通过纳米孔测序建立真菌元编码的质量过指南.
使用纳米孔数据评估两种标准的元编码方法 (基于参考的映射和98%的OTU集群).
为了研究腐烂的Fagus sylvatica树皮中的ectomycorrhizal社区.

主要方法:

纳米孔数据分析的eNano管道的开发和应用.
测试基于参考的映射与UNITE物种假设 (SH) 系统进行测试.
实施98%的操作分类单元 (OTU) 聚类.
在腐烂的Fagus sylvatica中对ectomycorrhizae进行案例研究分析,并补充了根尖形态化.

主要成果:

基于参考的映射和98%的OTU聚类都对纳米孔真菌元编码有效.
建议使用严格的映射标准来进行参考映射,而不是基于Phred的过.
对于98%的OTU方法,建议使用≥Q25的过读数.
腐烂梯度显著影响腐烂树皮中的真菌社区组成.
鉴定出Laccaria amethystina和Tomentella sublilacina是关键的生态菌.

结论:

纳米孔测序,配合适当的过指南,是真菌元编码和生态研究的宝贵工具.
UNITE SH系统在真菌元编码中增强了可复制性和研究间的通信.
纳米孔数据为真菌群落提供了重要的生态洞察力,例如腐烂木材中的生态菌群.

关键词:

野生花 (Fagus sylvatica) 是一种植物.一个纳米孔.弗雷德的得分得分是什么?死亡的树木木.在eNano管道上.结核病 (ectomycorrhiza) 是一种疾病.超级编码元标段编码.自然再生的自然再生.过的质量过的质量.

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