Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?
Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?
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DOI：
10.1186/s43008-020-00033-z
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发表时间：
2020-07-10
期刊：
影响因子：
5.4
通讯作者：
Schoch, Conrad L.
中科院分区：
文献类型：
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作者：
Luecking, Robert;Aime, M. Catherine;Schoch, Conrad L.
根据全球丰富度估计，真真菌（真菌）和真菌样生物（例如，菌虫门，卵菌门）构成了第二大生物群，预测约有300万种。与植物和动物相比，真菌具有简单的身体计划，通常在形态学和生态学上模糊不清的结构。这对准确和精确的识别提出了挑战。在这里，我们提供了一个概念性的框架，真菌的鉴定，鼓励物种界定的综合（多相）分类的方法，即系谱（遗传学），表型（包括autecology）和生殖生物学（可行时）的组合。这允许客观评价诊断特征，无论是表型或分子或两者。身份验证至关重要，但往往被忽视。由于分支特异性的进化历史，目前还没有单一的工具来识别真菌，尽管使用内部转录间隔区（ITS）的DNA条形码仍然是第一诊断，特别是在元条形码研究中。二级DNA条形码越来越多地用于ITS不能提供足够精确度的群体。成对序列相似性为基础的识别和OTU聚类的问题进行了讨论，并建议多个序列相似性为基础的系统发育方法与随后的验证更准确的替代品。在元条形码方法中，必须仔细考虑分子鉴定的速度和准确性和精确度之间的权衡。ITS和其他条形码标记的基因组内变异应适当记录，因为基因组类型多样性不一定是物种丰富度的代表。改进真菌的分子鉴定的重要策略是：（1）广泛地记录条形码标记的种内和基因组内变异;（2）显著地扩展序列库，集中于采样不足的进化枝和缺失的分类群;（3）改进初级库中的序列标签的策展，并且基于经验证的材料显著地增加序列的数量;（4）将序列数据链接到凭证标本的数字信息（包括图像）。与此同时，基因组测序的技术改进为未来DNA条形码提供了有前途的替代方案。尽管基于DNA的真菌分类学很流行，但基于表型的方法仍然是对真菌全球多样性进行分类和建立初始物种假设的重要策略。
True fungi (Fungi) and fungus-like organisms (e.g.Mycetozoa,Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.