Evaluation of the ribosomal DNA internal transcribed spacer (ITS), specifically ITS1 and ITS2, for the analysis of fungal diversity by deep sequencing.
Evaluation of the ribosomal DNA internal transcribed spacer (ITS), specifically ITS1 and ITS2, for the analysis of fungal diversity by deep sequencing.
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DOI：
10.1371/journal.pone.0206428
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Yao YJ
中科院分区：
文献类型：
--
作者：
Yang RH;Su JH;Shang JJ;Wu YY;Li Y;Bao DP;Yao YJ
核核糖体DNA内转录间隔区（ITS）已被广泛用于通过深度测序来评估不同环境中的真菌组成。为了评价ITS区在真菌多样性分析中的应用价值，本研究对ITS区不同片段测序结果进行了聚类和分类比较。从UNITE数据库中获得的83，120个全长ITS序列中，发现真菌界中ITS 1的平均变化大于ITS 2;这种变化包括长度和GC含量的变化和多态性，其中一些多态性是特定真菌群特有的。ITS的分类准确度高于ITS 1和ITS 2。常用的操作分类单位（OTU）用于评估真菌的多样性和丰富度分配几个物种到一个单一的OTU，即使在99.00%的序列相似性聚类。ITS 1和ITS 2之间的聚类和分类能力没有差异。然而，ITS 1和ITS 2之间的OTU共性非常低。为了进一步测试这一观察结果，从10个土壤样品中获得了219，741个焦磷酸测序读数，包括39，840个全长ITS序列，并将其聚类成OTU。焦磷酸测序结果与计算机分析的结果一致。ITS 1可能高估了真菌的多样性和丰富度。ITS，ITS 1和ITS 2的分析产生了几个不同的分类群，ITS和ITS 2的分类偏好是相似的。结果表明，在缺乏完整ITS序列的情况下，ITS 2可能是一个更适合揭示真菌群落操作分类学丰富度和分类学特征的标记。
The nuclear ribosomal DNA internal transcribed spacer (ITS) has been widely used to assess the fungal composition in different environments by deep sequencing. To evaluate the ITS in the analysis of fungal diversity, comparisons of the clustering and taxonomy generated by sequencing with different portions of the whole fragment were conducted in this study. For a total of 83,120 full-length ITS sequences obtained from the UNITE database, it was found that, on average, ITS1 varied more than ITS2 within the kingdom Fungi; this variation included length and GC content variations and polymorphisms, with some polymorphisms specific to particular fungal groups. The taxonomic accuracy for ITS was higher than that for ITS1 or ITS2. The commonly used operational taxonomic unit (OTU) for evaluating fungal diversity and richness assigned several species to a single OTU even with clustering at 99.00% sequence similarity. The clustering and taxonomic capacities did not differ between ITS1 and ITS2. However, the OTU commonality between ITS1 and ITS2 was very low. To test this observation further, 219,741 pyrosequencing reads, including 39,840 full-length ITS sequences, were obtained from 10 soil samples and were clustered into OTUs. The pyrosequencing results agreed with the results of the in silico analysis. ITS1 might overestimate the fungal diversity and richness. Analyses using ITS, ITS1 and ITS2 yielded several different taxa, and the taxonomic preferences for ITS and ITS2 were similar. The results demonstrated that ITS2 alone might be a more suitable marker for revealing the operational taxonomic richness and taxonomy specifics of fungal communities when the full-length ITS is not available.
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