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.

中文翻译：

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真菌的明确识别：我们处于什么位置以及真菌 DNA 条形码的准确度和精确度如何？

根据全球丰富度估计，真真菌（Fungi）和类真菌生物（例如霉菌纲、卵菌门）构成第二大生物类群，预计约有 300 万种。与植物和动物相比，真菌的身体结构简单，其形态和生态结构通常不明显。这对准确、精确的识别提出了挑战。在这里，我们提供了真菌鉴定的概念框架，鼓励采用综合（多相）分类学方法进行物种界定，即谱系学（系统发育）、表型（包括自生态学）和生殖生物学（如果可行）的结合。这允许客观评估表型或分子或两者的诊断特征。身份验证至关重要，但常常被忽视。由于分支特定的进化历史，目前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 条形码仍然是第一个诊断，特别是在元条形码研究中。二级 DNA 条形码越来越多地应用于 ITS 无法提供足够精度的群体。讨论了基于成对序列相似性的识别和 OTU 聚类的问题，并推荐基于多重序列比对的系统发育方法和后续验证作为更准确的替代方案。在元条形码方法中，必须仔细考虑分子识别的速度、准确度和精密度之间的权衡。ITS 和其他条形码标记的基因组内变异应正确记录，因为系统发育型多样性不一定代表物种丰富度。改善真菌分子鉴定的重要策略是：（1）广泛记录条形码标记的种内和基因组内变异；(2) 大幅扩展序列存储库，重点关注采样不足的进化枝和缺失的类群；(3) 改进主存储库中序列标签的管理，并大幅增加基于已验证材料的序列数量；(4) 将序列数据链接到凭证样本的数字信息（包括图像）。与此同时，基因组测序技术的进步为未来 DNA 条形码提供了有希望的替代方案。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全球真菌多样性进行分类和建立初始物种假设的重要策略。