T443__283__rbcL
Each of the 688 samples was pulverized using TissueLyser II (Qiagen) and then host plant and fungal symbiont DNA was extracted with the cetyltrimethylammonium bromide method.
The obtained fungal and plant PCR products were pooled afterpurification with AMPure XP Kit (Beckman Coulter) and the pooledlibrary was subjected to an Illumina Miseq run with the 2 x 300 cyclesequencing kit (version 3). To prevent the potential demultiplexingerrors, we converted the raw MiSeq BCL data into FASTQ data byourselves using the bcl2fastq v1.8.4 program distributed by Illuminaand we then demulitiplexed the FASTQ data using the program Claidentv0.2.2015.03.11 (Tanabe and Toju, 2013; Tanabe, 2015). In thedemultiplexing process with Claident, all the sequencing readscontaining low quality (quality scores less than 30) index sequences wereeliminated and no mismatch between input and output index sequenceswas tolerated. The remaining forward and reverse sequencing reads werethen fused with each other by the program PEAR v0.9.6 (Zhang et al.,2014) with a stringent threshold for merging (p = 0.0001). Among thepaired-end reads obtained, we discareded those less than 150 bp inlength and those for which 10% or more of nucleotides had low (less than 30) quality values.