Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected.

中文翻译：

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NGS条码测序在分类学和诊断学中的应用，具有宏基因组学的观点，在“ Candida”病原性酵母中的应用。

酵母和其他真菌的物种鉴定目前使用选定分子标记的Sanger序列进行，主要来自核糖体DNA操纵子，其特征是18S，ITS1、5.8S，ITS2和LSU基因座的数百个串联重复序列。ITS区域最近被提议作为主要的条形码标记，使该区域成为分类学，系统发育和诊断学中使用最多的区域。NGS的引入提供了高效且低成本的工具，可同时扩增两个或多个标记，并具有很高的测序深度。然而，重复之间存在基因组内变异性需要特定的分析程序和流程。在这项研究中，用NGS分析了属于11种致病酵母菌的286个菌株，该区域的范围从ITS1到编码核糖体DNA的LSU的D1 / D2结构域。结果表明，相对较高的异质性可能会阻碍这些序列用于鉴定单个菌株，甚至鉴定更多复杂的微生物混合物。这些观察指出，宏基因组学研究可能会受到物种拐弯的影响，其水平高于目前的预期。