Modern taxonomy has developed towards the establishment of global authoritative lists of species that assume the standardized principles of species recognition, at least in a given taxonomic group. However, in fungi, species delimitation is frequently subjective because it depends on the choice of a species concept and the criteria selected by a taxonomist. Contrary to it, identification of fungal species is expected to be accurate and precise because it should predict the properties that are required for applications or that are relevant in pathology. The industrial and plant-beneficial fungi from the genus Trichoderma (Hypocreales) offer a suitable model to address this collision between species delimitation and species identification. A few decades ago, Trichoderma diversity was limited to a few dozen species. The introduction of molecular evolutionary methods resulted in the exponential expansion of Trichoderma taxonomy, with up to 50 new species recognized per year. Here, we have reviewed the genus-wide taxonomy of Trichoderma and compiled a complete inventory of all Trichoderma species and DNA barcoding material deposited in public databases (the inventory is available at the website of the International Subcommission on Taxonomy of Trichoderma www.trichoderma.info). Among the 375 species with valid names as of July 2020, 361 (96%) have been cultivated in vitro and DNA barcoded. Thus, we have developed a protocol for molecular identification of Trichoderma that requires analysis of the three DNA barcodes (ITS, tef1, and rpb2), and it is supported by online tools that are available on www.trichokey.info. We then used all the whole-genome sequenced (WGS) Trichoderma strains that are available in public databases to provide versatile practical examples of molecular identification, reveal shortcomings, and discuss possible ambiguities. Based on the Trichoderma example, this study shows why the identification of a fungal species is an intricate and laborious task that requires a background in mycology, molecular biological skills, training in molecular evolutionary analysis, and knowledge of taxonomic literature. We provide an in-depth discussion of species concepts that are applied in Trichoderma taxonomy, and conclude that these fungi are particularly suitable for the implementation of a polyphasic approach that was first introduced in Trichoderma taxonomy by John Bissett (1948–2020), whose work inspired the current study. We also propose a regulatory and unifying role of international commissions on the taxonomy of particular fungal groups. An important outcome of this work is the demonstration of an urgent need for cooperation between Trichoderma researchers to get prepared to the efficient use of the upcoming wave of Trichoderma genomic data.

现代分类学已朝着建立全球物种权威列表的方向发展，这些列表至少在给定的分类学组中采用了物种识别的标准化原则。但是，在真菌中，物种划分通常是主观的，因为它取决于物种概念的选择和分类学家选择的标准。与此相反，真菌种类的鉴定被期望是准确和精确的，因为它应该预测应用所需的性质或与病理相关的性质。木霉属（Hypocreales）的工业和植物有益真菌提供了一个合适的模型来解决物种界定和物种识别之间的冲突。几十年前，木霉多样性仅限于几十种。分子进化方法的引入导致木霉分类学的指数扩展，每年确认多达50个新物种。在这里，我们已经回顾了木霉属的全属分类学，并整理了所有木霉属物种的完整清单，以及存放在公共数据库中的DNA条形码材料（该清单可在国际木霉菌分类小组委员会的网站上找到，网址为www.trichoderma.info。 ）。截至2020年7月，有效名称的375种中，有361种（96％）已在体外培养并用DNA条码编码。因此，我们开发了用于木霉属分子鉴定的方案这需要分析三个DNA条形码（ITS，tef1和rpb2），并且它由www.trichokey.info上可用的在线工具支持。然后，我们使用公共数据库中提供的所有全基因组测序（WGS）木霉菌株，提供分子鉴定的通用实用示例，揭示不足之处，并讨论可能的歧义。以木霉属菌为例，该研究表明为什么鉴定真菌物种是一项复杂而费力的任务，需要真菌学背景，分子生物学技能，分子进化分析培训和分类学文献知识。我们深入讨论了应用于木霉菌分类学，并得出结论，这些真菌特别适用于多相方法的实施，这是约翰·比塞特（John Bissett，1948–2020年）在木霉菌分类学中首次引入的，他的工作启发了当前的研究。我们还建议国际委员会对特定真菌群体的分类法起规范和统一的作用。这项工作的重要成果是证明了木霉属研究人员之间迫切需要合作，以为有效利用即将来临的木霉基因组数据浪潮做好准备。