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.