Many studies describing communities of arbuscular mycorrhizal fungi (AMF, Glomeromycota) based on high-throughput sequencing target the V4 variable region of the 18S ribosomal gene. However, an accurate taxonomic assignment of these short 18S sequences is challenging. Here we describe a simple approach based on a phylogenetic analysis using a backbone of reference sequences with taxonomic names updated in MycoBank to improve the taxonomic assignment of amplicon sequence variants (ASVs). As a case study, paired-end sequencing (2 × 250 bp) was carried out to describe the community of AMF associated with Tamarix aphylla from Algerian steppe ecosystems. AMF from root and soil samples were targeted with a nested PCR, using the AMF-discriminating primers pair AML1/AML2 for the first amplification and a new primer pair for the second. The proportion of the sequences assigned to Glomeromycota was 85.9%, representing a total of 87 ASVs. Seven well-defined genera (Claroideoglomus, Dominikia, Funneliformis, Innospora, Microkamienskia, Rhizophagus, Septoglomus) and seven phylogenetic divergent clades of Glomus (27% of the ASVs) were identified with the proposed approach. This taxonomic assignment was in sharp contrast with querying the MaarjAM or GenBank databases. Out-of-date taxonomy led the MaarjAM database to attribute 85% of the ASVs to the genus Glomus and the GenBank database to assign 18% of the ASVs to unclassified taxa. We recommend using the simple workflow presented in this study so that up-to-date taxonomic information is accurately assigned to AMF communities analyzed by high-throughput sequencing.

中文翻译：

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在18S宏基因组数据集中的丛枝菌根真菌的分类学分配：以柳杉（Tamarix aphylla）为例的研究。

许多研究基于高通量测序来描述丛枝菌根真菌（AMF，Glomeromycota）群落，这些研究针对18S核糖体基因的V4可变区。但是，对这些短的18S序列进行准确的分类分配是一项挑战。在这里，我们描述了一种基于系统进化分析的简单方法，该系统使用参考序列的主干以及MycoBank中更新的分类名称来改善扩增子序列变体（ASV）的分类分配。作为案例研究，进行了双末端测序（2×250 bp）来描述与with柳相关的AMF群落来自阿尔及利亚的草原生态系统。使用嵌套式PCR靶向根和土壤样品中的AMF，首先使用AMF区分引物对AML1 / AML2，第二次使用新的引物对。分配给glomeromycota的序列的比例是85.9％，代表总共87个ASV。七良好定义的属（Claroideoglomus，Dominikia，Funneliformis，Innospora，Microkamienskia，Rhizophagus，Septoglomus）和七个系统发生进化支发散球囊霉（27％的ASV）是通过建议的方法确定的。这种分类分配与查询MaarjAM或GenBank数据库形成鲜明对比。过时的分类法导致MaarjAM数据库将85％的ASV归因于Glomus属，而GenBank数据库将18％的ASV归因于未分类的分类群。我们建议使用本研究中介绍的简单工作流程，以便将最新分类学信息准确分配给通过高通量测序分析的AMF社区。