ITS1 versus ITS2 as DNA metabarcodes for fungi

The nuclear ribosomal Internal Transcribed Spacer ITS region is widely used as a DNA metabarcoding marker to characterize the diversity and composition of fungal communities. In amplicon pyrosequencing studies of fungal diversity, one of the spacers ITS1 or ITS2 of the ITS region is normally used. In this methodological study we evaluate the usability of ITS1 vs. ITS2 as a DNA metabarcoding marker for fungi. We analyse three data sets: two comprising ITS1 and ITS2 sequences of known taxonomic affiliations and a third comprising ITS1 and ITS2 environmental amplicon pyrosequencing data. Clustering analyses of sequences with known taxonomy using the bioinformatics pipeline ClustEx revealed that a 97% similarity cut-off represent a reasonable threshold for estimating the number of known species in the data sets for both ITS1 and ITS2. However, no single threshold value worked well for all fungi at the same time within the curated UNITE database, and we found that the Operational Taxonomic U...

核糖体核内转录间隔区（Internal Transcribed Spacer，ITS）区域被广泛用作DNA宏条形码标记，用于表征真菌群落的多样性与组成。在真菌多样性的扩增子焦磷酸测序研究中，通常会选用ITS区域的ITS1或ITS2其中一个间隔区作为扩增靶点。本方法学研究旨在评估ITS1与ITS2作为真菌DNA宏条形码标记的应用可行性。我们共分析了三套数据集：两套包含具有已知分类学归属的ITS1与ITS2序列，第三套则包含ITS1与ITS2的环境扩增子焦磷酸测序数据。通过生物信息学流程ClustEx对携带已知分类学信息的序列进行聚类分析后发现，对于ITS1与ITS2而言，97%的相似性截断阈值均为合理阈值，可用于估算数据集中已知物种的数量。然而，在经人工整理注释的UNITE数据库中，并无单一阈值可同时适用于所有真菌类群，且我们发现操作分类单元（Operational Taxonomic Unit，OTU）……