Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
World J Microbiol Biotechnol. 2023 Jun 21;39(9):229. doi: 10.1007/s11274-023-03678-1.
Metabarcoding using high throughput sequencing of amplicons of the 18S rRNA gene is one of the widely used methods for assessing the diversity of microeukaryotes in various ecosystems. We investigated the effectiveness of the V4 and V8-V9 regions of the 18S rRNA gene by comparing the results of metabarcoding microeukaryotic communities using the DADA2 (ASV), USEARCH-UNOISE3 (ZOTU), and USEARCH-UPARSE (OTU with 97% similarity) algorithms. Both regions showed similar levels of genetic variability and taxa identification accuracy. Richness for DADA2 datasets of both regions was lower than for UNOISE3 and UPARSE datasets, which is due to more accurate error correction in amplicons. Microeukaryotic communities (autotrophs and heterotrophs) structure identified using both regions showed a significant relationship with phytoplankton (autotrophs) communities structure based on microscopy in a seasonal freshwater sample series. The strongest relationship was found between the phytoplankton species and V8-V9 ASVs produced by DADA2.
基于高通量测序扩增 18S rRNA 基因的宏条形码技术是评估各种生态系统中微型真核生物多样性的常用方法之一。我们通过比较 DADA2（ASV）、USEARCH-UNOISE3（ZOTU）和 USEARCH-UPARSE（相似度为 97%的 OTU）算法对微真核生物群落进行宏条形码分析的结果，研究了 18S rRNA 基因 V4 和 V8-V9 区的有效性。这两个区域都显示出相似的遗传变异和分类准确性。DADA2 数据集的丰富度两个区域均低于 UNOISE3 和 UPARSE 数据集，这是由于扩增子中进行了更准确的错误校正。使用两个区域鉴定的微真核生物群落（自养生物和异养生物）结构与基于显微镜的季节性淡水样本系列中的浮游植物（自养生物）群落结构之间存在显著关系。在浮游植物物种和 DADA2 产生的 V8-V9 ASVs 之间发现了最强的关系。
