Identification of Arbuscular Mycorrhizal Fungal Isolates using MiSeq Sequencing

The standardization of strain identification methods is essential for effectively managing the genetic resources of arbuscular mycorrhizal (AM) fungi. Due to their highly polymorphic rRNA sequence and multinucleate nature, conventional strain identification using a single sequence of the rRNA region is often inadequate for these fungi. Therefore, the present study exami-ned the use of genetic diversity information obtained through high-throughput sequencing to improve the strain identification of AM fungal isolates. Five previously reported primer pairs were used to amplify a portion of the rRNA region from DNA extracted from AM fungal spores, which was then sequenced using the Illumina MiSeq platform. The majority of amplicon sequence variants (ASVs) matched the same strain as the source isolate. A cluster anal-ysis indicated that strains of the same species generally grouped together, demonstrating the method's effectiveness for species-level identification. Furthermore, a phylogenetic anal-ysis revealed some strain-specific ASVs that may be valuable for differentiating between different strains within the same species. Based on these results, it is feasible to develop a reliable identification protocol for AM fungal isolates using MiSeq sequencing.