Sequence variation in nuclear ribosomal SSU, ITS and LSU regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate-dependent

Eight replicate DNA extrctions were performed, each from three spores of R. irregularis DAOM197198 and subjected to whole genome amplification with the REPLI-g Mini kit (Qiagen) according to the manufacturer's instructions. Library fragments with sizes ranging from 700 bp to 800 bp were purified by gel electrophoresis, and the fragment length of the library was verified using Bioanalyzer (Agilent Technologies, Santa Clara, USA). Library was validated by qPCR using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, USA) in order to optimize cluster generation and sequenced on one lane of a HiSeq2000 v3 flowcell (Illumina, San Diego, USA), with paired-end (PE), 100-bp reads at the Illumina CSPro lab of the Estonian Genome Centre, University of Tartu, Estonia. Demultiplexing allowing 1 mismatch was carried out using CASAVA (Illumina, San Diego, USA), yielding 115M read-pairs with 85% of bases with quality = Q30.