Utilizing ITS1 and ITS2 to study environmental fungal diversity using pyrosequencing
Utilizing ITS1 and ITS2 to study environmental fungal diversity using pyrosequencing
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DOI：
10.1111/1574-6941.12046
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发表时间：
2013-04-01
影响因子：
4.2
通讯作者：
Stenlid, Jan
中科院分区：
文献类型：
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作者：
Monard, Cecile;Gantner, Stephan;Stenlid, Jan
高通量测序产生的较短读段导致真菌多样性分析中关注ITS 1或ITS 2亚位点。我们的研究旨在确定做出这种选择将如何影响所获得的数据集以及我们对环境真菌多样性的看法。从不同的环境样品（水，沉积物和土壤）中提取DNA，扩增总的内转录间隔区（ITS）位点。454-以ITS 1和ITS 2为靶进行测序。在ITS 2数据集中没有检测到序列数量、操作分类单位（OTU）和优势OTU的显著差异，但观察到较少的多样性。在土壤样品中，真菌分类鉴定的差异进行了观察，更多的担子菌在ITS 1数据集和更多的子囊菌在ITS 2数据集。在两个数据集中仅检测到三分之一的OTU，这可能是由于（1）在ITS 2数据集中去除了更多的短序列，（2）取决于用作BLASTn查询的亚基因座的不同分类学归属和/或（3）引物如何扩增真实群落的选择性。虽然ITS 1和ITS 2数据集在真菌群落水平上得出了类似的结果，但为了进一步深入分析多样性，本研究建议对两个ITS区域进行分析，因为它们提供了不同的信息，并且是互补的。
The shorter reads generated by high-throughput sequencing has led to a focus on either the ITS1 or the ITS2 sublocus in fungal diversity analyses. Our study aimed to determine how making this choice would influence the datasets obtained and our vision of environmental fungal diversity. DNA was extracted from different environmental samples (water, sediments and soil) and the total internal transcribed spacer (ITS) locus was amplified. 454-sequencing was performed targeting both ITS1 and ITS2. No significant differences in the number of sequences, operational taxonomic units (OTUs) and in the dominant OTUs were detected but less diversity was observed in the ITS2 dataset. In the soil samples, differences in the fungal taxonomic identification were observed, with more Basidiomycota in the ITS1 dataset and more Ascomycota in the ITS2 dataset. Only one-third of the OTUs were detected in both datasets which could be due to (1) more short sequences removed in the ITS2 dataset, (2) different taxonomic affiliation depending on the sublocus used as BLASTn query and/or (3) selectivity in how a primer amplifies the true community. Although ITS1 and ITS2 datasets led to similar results at the fungal community level, for further in-depth diversity analysis this study suggests the analysis of both ITS regions, as they provided different information and were complementary.