Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography
Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography
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DOI：
10.1007/s00248-021-01730-x
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发表时间：
2021-03
影响因子：
3.6
通讯作者：
Laura Tipton;Geoffrey L. Zahn;J. L. Darcy;A. Amend;Nicole A. Hynson
中科院分区：
文献类型：
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作者：
Laura Tipton;Geoffrey L. Zahn;J. L. Darcy;A. Amend;Nicole A. Hynson
为了研究包括真菌在内的微生物的地理学和其他生态模式，科学家们一直使用操作分类单位（OTU）作为物种或物种假设的代表。然而，当通过在可接受的条形码基因座（例如细菌中的16S或真菌中的ITS）处的97%序列相似性截止值来定义时，这些OTU可以模糊生物学模式，掩盖分类学多样性，并阻碍荟萃分析。已经提出了扩增子序列变体（ASV）来缓解所有这些问题，并且已经在细菌中证明了这一点。分析ASV刚刚成为真菌研究中的一种常见做法，目前还不清楚使用这种方法在细菌研究中发现的益处是否会转移到真菌中。在这里，我们通过分析ITS1扩增子测序数据作为ASV并探索生态模式对夏威夷真菌进行了荟萃分析。这些调查涵盖了三个岛屿群和五个生态系统，合并成第一个全面的夏威夷真菌生物群ASV数据库。我们的研究结果表明，ASV可以用于联合收割机真菌ITS调查，提高再现性，并保持广泛的生态模式与OTU观察到的，包括多样性排序。此外，在我们的数据库中，包括一些最常见的OTU的ASV揭示了一些岛屿专家，这表明传统的OTU聚类可以掩盖重要的地理模式。我们建议未来的真菌研究，特别是那些旨在评估真菌谱的研究，分析ASV而不是OTU。我们的结论是，类似于细菌研究，ASVs提高了真菌研究的重现性和数据共享。
To study biogeography and other ecological patterns of microorganisms, including fungi, scientists have been using operational taxonomic units (OTUs) as representations of species or species hypotheses. However, when defined by 97% sequence similarity cutoff at an accepted barcode locus such as 16S in bacteria or ITS in fungi, these OTUs can obscure biogeographic patterns, mask taxonomic diversity, and hinder meta-analyses. Amplicon sequence variants (ASVs) have been proposed to alleviate all of these issues and have been shown to do so in bacteria. Analyzing ASVs is just emerging as a common practice among fungal studies, and it is unclear whether the benefits found in bacterial studies of using such an approach carryover to fungi. Here, we conducted a meta-analysis of Hawaiian fungi by analyzing ITS1 amplicon sequencing data as ASVs and exploring ecological patterns. These surveys spanned three island groups and five ecosystems combined into the first comprehensive Hawaiian Mycobiome ASV Database. Our results show that ASVs can be used to combine fungal ITS surveys, increase reproducibility, and maintain the broad ecological patterns observed with OTUs, including diversity orderings. Additionally, the ASVs that comprise some of the most common OTUs in our database reveals some island specialists, indicating that traditional OTU clustering can obscure important biogeographic patterns. We recommend that future fungal studies, especially those aimed at assessing biogeography, analyze ASVs rather than OTUs. We conclude that similar to bacterial studies, ASVs improve reproducibility and data sharing for fungal studies.