PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi

There is no consensus barcoding region for determination of arbuscular mycorrhizal fungal (AMF) taxa. To overcome this obstacle, we have developed an approach to sequence AMF marker within the ribosome-encoding operon (rDNA) that covers all three widely applied variable molecular markers. Using a nested PCR specific AMF, amplified part (c. 2.5 kb) rDNA spanning majority small subunit rRNA (SSU) gene, complete internal transcribed spacer (ITS) and large (LSU) gene. The products were sequenced on PacBio platform utilizing Single Molecule Real Time (SMRT) sequencing. Employing method selected environmental DNA samples, able describe complex communities consisting various glomeromycotan lineages. We demonstrate applicability new kb provide robust phylogenetic assignment lineages without known sequences from pure cultures consolidate information about taxon distributions coming used regions into one integrative dataset.