title: WATERLOGGING3
design: Illumina sequencing (San Diego, CA, USA) was performed by Novogene Co. Ltd (Cambridge, United Kingdom), after checking total RNA quantity and quality on an Agilent 5400 Fragment Analyzer System (Santa Clara, CA, United States). Raw data (in FASTq format) were processed and Q30 values and GC contents were measured. After removing low-quality reads, the remaining clean data were used for all downstream analyses. HISAT2 algorithm (v 2.0.5) was used to map the filtered sequenced reads to the reference genome, the manually curated A. chinensis var. chinensis Red5 genome (Pilkington et al. 2018). Transcripts were assembled by StringTie software (v1.3.3) and differentially expressed gene (DEG) analysis was performed using the DESeq2 R package (Anders et al., 2010).