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.

BambooBase:A comprehensive database of bamboo omics and systematics

Dear Editor,Bamboos(Bambusoideae,Poaceae)are of significant economic and ecological importance,supporting billions of people and contributing to international trade(Wu et al.,2023).They play a crucial role in carbon fixation and support a multitude of other species including the giant panda(Clark et al.,2015).Since the release of the first draft genome of moso bamboo(Phyllostachys edulis)(Peng et al.,2013),there has been a notable increase in the sequencing,assembly,and annotation of diverse bamboo genomes(Guo et al.,2019;Zheng et al.,2022;Ma et al.,2024).An existing resource for bamboo genomics,BambooGDB(Zhao et al.,2014),provides information based on the individual draft reference genome of moso bamboo.What is needed,however,is a resource reinforcing multiple genome assemblies in Bambusoideae to enable researchers to unravel the evolutionary history of chromosomes and genes through cladespecific comparative genomic investigations.Here,we present BambooBase(https://bamboo.genobank.org/),a newly developed web-based database designed to provide a seamless user experience for bamboo omics and systematics.