RNA-seq root: D7_replicate2
we used the Illumina TruSeq stranded mRNA kit and the sequencing was done with the Illumina NovaSeq6000 system (100 bp paired-end sequencing, 3 Gb/sample). To estimate gene expression based on RNA-seq, Trimmomatic was used to clean the raw reads and quality-controlled reads were aligned to IRGSP 1.0 using the Hisat2 aligner. The sequence reads were mapped to genomic features using featureCounts, and normalization of reads was carried out using the DESeq2 package.