Total RNA was isolated from the whole Arabidopsis seedlings using RNeasy plant mini kits (Qiagen). mRNA was extracted from total RNA using Dynabeads oligo (dT) (Invitrogen Dynal). First- and second-strand cDNAs were generated using SuperScript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNAs were fragmented by nebulization and used for RNA-seq library construction following the NovaSeq protocol.