Data from: 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 Unit (OTU) concept is not easily translated into the level of species because many species are distributed over several clusters. Clustering analyses of the 134 692 ITS1 and ITS2 pyrosequences using a 97% similarity cut-off revealed a high similarity between the two data sets when it comes to taxonomic coverage. Although some groups are under- or unrepresented in the two data sets due to, e.g. primer mismatches, our results indicate that ITS1 and ITS2 to a large extent yield similar results when used as DNA metabarcodes for fungi.细胞核核糖体DNA内部转录间隔区（Internal Transcribed Spacer, ITS）被广泛用作DNA元条形码标记，以解析真菌群落的多样性与组成。在真菌多样性扩增子焦磷酸测序研究中，通常会选用ITS区域中的ITS1或ITS2间隔区。本项方法学研究旨在评估ITS1与ITS2作为真菌DNA元条形码标记的实用性。我们共分析了三类数据集：两类包含已知分类学归属的ITS1与ITS2序列，第三类则包含ITS1与ITS2的环境扩增子焦磷酸测序数据。使用生物信息学流程ClustEx对已知分类学归属的序列进行聚类分析后发现，对于ITS1与ITS2两类数据集而言，97%的相似性阈值均为估算已知物种数量的合理阈值。然而，在经过人工整理的UNITE数据库中，不存在可同时适配所有真菌类群的单一阈值；同时我们发现，操作分类单元（Operational Taxonomic Unit, OTU）这一概念难以直接对应至物种层级，因为诸多物种会分布于多个聚类簇中。对134692条ITS1与ITS2焦磷酸测序序列采用97%相似性阈值开展聚类分析后结果显示，两类数据集在分类覆盖度方面表现出高度相似性。尽管由于引物错配等因素，部分类群在两个数据集中存在覆盖不足或未被覆盖的情况，但本研究结果表明，将ITS1与ITS2作为真菌DNA元条形码时，二者在很大程度上可得到相近的分析结果。