1605F32
The PCR products for each sample were pooled and purified using a PCR fragment purification kit (TaKaRa, Japan). The library was prepared using TruSeqTM DNA Sample Prep Kit and then sequenced on the Illumina MiSeq platform (Illumina, USA). The raw MiSeq BCL data was converted into FASTQ data using the bcl2fastq program distributed by Illumina and then the FASTQ data was demulitiplexed using the script demultiplex_fasta.py in QIIME (Caporaso et al., 2010). After the demultiplexing process, the raw forward and reverse reads were performed quality control with a classic threshold (TRAILING:20; SLIDINGWINDOW:50:20; MINLEN:51; AVGQUAL:25). Subsequently, the remaining forward and reverse sequencing reads were paired with FLASH using default settings (Magoc et al., 2011).