2.4.2 Sequencing data processing
Raw sequence data were quality-filtered, and chimera was checked using
the QIIME software (version 1.8.0) to remove reads containing more than
10% unknown nucleotides and reads where fewer than 50% of all bases
had quality values (Q-values) >20 (Caporaso et al .,
2010). Operational taxonomic units (OTUs) were clustered with a sequence
threshold of 97% similarity by UPARSE39, and representative sequences
of OTUs were picked up simultaneously. The tag sequence with the highest
abundance within each cluster was selected as the representative
sequence. The taxonomic assignment of 16S rRNA sequences was determined
using the bacterial SSUrRNA reference database with the Mothur and SILVA
(http://www.arb-silva.de/) classifier, and ITS sequences was determined
using the Unite reference database (http://unite. ut.ee/index.php) with
the Ribosomal Database Project (RDP) classifier at a 97% level (Edgaret al ., 2011).