Temporal regulation of alternative splicing events in rice memory under drought stress

Plant adaptation to drought stress is essential for plant survival and crop yield.Recently,harnessing drought memory,which is induced by repeated stress and recovery cycles,was suggested as a means to improve drought resistance at the transcriptional level.However,the genetic mechanism underlying drought memory is unclear.Here,we carried out a quantitative analysis of alternative splicing(AS)events in rice memory under drought stress,generating 12 transcriptome datasets.Notably,we identified exon skipping(ES)as the predominant AS type(>80%)in differential alternative splicing(DAS)in response to drought stress.Applying our analysis pipeline to investigate DAS events following drought stress in six other plant species revealed variable ES frequencies ranging from 9.94%to 60.70%depending on the species,suggesting that the relative frequency of DAS types in plants is likely to be speciesspecific.The dinucleotide sequence at AS splice sites in rice following drought stress was preferentially GC-AG and AT-AC.Since U12-type splicing uses the AFAC site,this suggests that drought stress may increase U12-type splicing,and thus increase ES frequency.We hypothesize that multiple isofbrms derived from exon skipping may be induced by drought stress in rice.We also identified 20 transcription factors and three highly connected hub genes with potential roles in drought memory that may be good targets for plant breeding.

R-loopAtlas:An integrated R-loop resource from 254 plant species sustained by a deep-learningbased tool

R-loops are chromatin structures consisting of anRNA:DNA hybrid and the other single-stranded DNA,which widely exist among genomes from bacteria to higher eukaryotes and participate in a variety of biological processes(Zhou et al.,2022).Currently,a variety of approaches to detect genome-wide R-loops have been developed,and ssDRIP-seq(single-strand DNA ligation-based library preparation from DNA:RNA hybrid immunoprecipitation,followed by sequencing)is one of the widely utilized methods(Xu et al.,2022).However,there are many limitations to genome-wide R-loop mapping based on high-throughput methods.For example,the activity of restriction enzymes for genomic DNA fragmentation.