2.7 Transcriptome analysis
Raw data (raw reads) in FASTQ format were first processed through
primary quality control. In this step, clean data (clean reads) were
obtained by removing reads containing adapters, reads containing poly-N,
low-quality reads (lower than 5) and contaminants from the raw data. All
downstream analyses were based on clean data of a high quality.
Paired-end clean reads were aligned to the assembled genome of M.
dirhodum using TopHat with default parameters. Differential expression
analysis was performed using the DEGSeq R package (1.20.0) (Wang et al.,
2010). We used the adjusted P value (padj) ≤ 0.001 and a
|log (fold-change)| ≥ 2 as the criteria for the
significant difference in expression.