HTS data processing
The sequencing process provided 22 demultiplexed raw fastq files. For
each file, the quality of raw data was assessed using FastQC tools
(Andrews, 2010). Each set of paired ends reads were merged into a single
sequence using the VSEARCH software (Rognes, Flouri, Nichols, Quince, &
Mahé, 2016). The minimum length of the overlap region between the reads
was at least 36 bp, and the overlap region should not include more than
3 mismatches and 5 ambiguous bases. Next, primers were trimmed off using
the trim_oligos.pl software (Sáenz de Miera; not published). Then, poor
quality sequencing reads were filtered out according to the following
parameters: minimum length = 251 bp, maximum length = 272 bp and Phred
quality score = 35 using VSEARCH (Rognes et al., 2016). Next, the
identical sequences were dereplicated to obtain Independent Sequence
Units (ISUs). Finally, the UCHIME algorithm of VSEARCH (Rognes et al.,
2016) was used to remove chimeric sequences.