Leaf age determines flood resilience through distinct submergence and recovery effects

RNA sequencing (RNA-seq) was performed to investigate potential roles of the unfolded protein response in submergence and recovery responses of Arabidopsis thaliana. Plants were grown to the 10-leaf stage and then subjected to 4 days of complete submergence. Samples were collected at four time points: prior to submergence (T0), after 1 day of submergence (1d), after 4 days of submergence (4d - end of submergence period), and 3 hours after de-submergence (recovery). For each time point, rosettes were collected and divided into two developmental zones: (i) old leaves (leaves 1 to 5) and (ii) young leaves (leaves 6 to 10 including the shoot apical meristem (SAM)). There were three biological replicates per tissue type of each genotype at each time point. Each biological replicate consisted of tissue pooled from two plants. Two genotypes were examined: Col-0 (wild type) and the bzip60/bzip28 double mutant, which is impaired in unfolded protein response signaling. RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA protocol and sequenced on an Illumina platform to generate paired-end reads.