NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective.
NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective.
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DOI：
10.5598/imafungus.2018.09.01.07
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发表时间：
2018-06
期刊：
影响因子：
5.4
通讯作者：
Cardinali G
中科院分区：
文献类型：
--
作者：
Colabella C;Corte L;Roscini L;Bassetti M;Tascini C;Mellor JC;Meyer W;Robert V;Vu D;Cardinali G
酵母和其它真菌的物种鉴定目前是用所选分子标记的桑格序列进行的，所选分子标记主要来自核糖体DNA操纵子，其特征在于18 S、ITS 1、5.8S、ITS 2和LSU基因座的数百个串联重复。ITS区最近已被提出作为主要的条形码标记，使该区域在分类学，遗传学和诊断学中最常用的一个。NGS的引入提供了高效率和相对低成本的工具，以同时扩增两个或更多个标记物，具有很大的测序深度。然而，重复序列之间基因组内变异的存在需要特定的分析程序和管道。在这项研究中，286株属于11种致病性酵母菌进行了分析与NGS的区域从ITS 1的LSU编码核糖体DNA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一菌株甚至更多复杂微生物混合物。这些观察结果指出，宏基因组学研究可能受到物种变异的影响，其程度高于目前的预期。
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.