2.4.2 RNA-seq reads, pre-processing and alignment
The raw paired-end reads were trimmed and quality controlled by Fastp with default parameters (Chen et al., 2018). And then, clean data from the samples were used to perform de novo assembly with Trinity (Grabherr et al., 2011). To increase the assembly quality, all the assembled sequences were filtered by CD-Hit. To obtain the number of reads compared to the assembled transcripts which were used for subsequent expression analysis, the clean reads of each sample were compared with the reference sequence obtained from the Trinity assembly using Bowtie2.