Bioinformatics Analysis Of Gene Expression And Pre-mRNA Alternative Splicing In Arabidopsis Thaliana

In eukaryotes,alternative pre-mRNA splicing is an important regulatory mechanism for gene expression,and is the major contributor to proteome diversity.Alternative splicing is regulated by many factors such as cis-acting sequence elements,trans-acting protein factors,and histone modifications,etc.Alternative splicing plays a pivotal role in tissue differentiation,development,and disease,etc.In recent years,alternative splicing has become the research focus of biology.With the rapid development of next-generation sequencing technologies such as RNA-seq,a large number of alternative splicing events from multi-exon genes have been detected.In humans,over 95% of multi-exon genes undergo alternative splicing.In plant genomes including Arabidopsis thaliana,Oraza sativa,and Zea mays,over 60% of multi-exon genes are alternatively spliced.So far,alternative splicing has been studied extensively in animal genomes such as human,mouse etc.However,the work focused on alternative splicing of plant genomes is relatively fewer.Plant transcriptome studies showed that pre-mRNA alternative splicing is closely related to biological processes such as tissue differentiation,organ development,and environmental stress,etc.In this study,we analyzed gene expression and alternative spicing in different tissues and environmental stresses of Arabidopsis by utilizing the RNA-seq data in the public database(GEO).The detailed research contents are summarized as follows:Firstly,gene expression and alternative splicing were analyzed in different tissues of Arabidopsis.Based on RNA-seq sequencing data,using the tools of Trimmomatic,Salmon,DESeq2,SUPPA2 and other tools,the atlas of gene expression and alternative splicing events in seeds,roots,leaves,flowers,pedicels,internodes and pods were established.Furthermore,differentially expressed genes and differentially alternative splicing events were identified between different tissues.Then,the biological functions of related genes were analyzed.It was indicated that the regulation of the floral organ development in Arabidopsis can be modulated by the usage of differential alternative splicing.It can be deduced alternative splicing exerts a crucial role in the development and differentiation of plant tissues and organs.Secondly,gene expression and alternative splicing were analyzed during seed germination of Arabidopsis.First of all,by using Hisat2,StringTie,DESeq2 and other tools,we created the gene expression matrix and identify differentially expressed genes between dry seeds,germinating seeds1-3,young seeds and seeds in Arabidopsis.The results showed that many genes involved in metabolic processes,such as glycolysis and DNA synthesis,were activated during the seed germination.It ensures the reactivation of metabolism and basic cellular activities of seeds.Some genes involved in environmental responses,such as oxidative stress,toxic substance,heat,and water,were inhibited.This is essential for seeds to be successfully activated from a dormant state.Furthermore,rMATS was utilized to detect the pre-mRNA alternative splicing events and differential alternative splicing events under different conditions.We also profiled the feature of alternative splicing events and analyzed the biological functions of differential alternative splicing events during seed germination.Thirdly,gene expression and alternative splicing were analyzed in Arabidopsis leaf tissue under cold stress.RNA-seq sequencing data of Arabidopsis leaf tissue under cold stress at 4 ° C for0 hours,1 hour,3 hours,6 hours,12 hours,and 24 hours was used as the raw dataset.The tools including Trimmomatic,Salmon,DESeq2,and SUPPA2,were used to identify expressed genes and alternative splicing events under various stress conditions.Moreover,differentially expressed genes and differentially alternative splicing events were identified between different stress conditions.Besides,the biological functions of differentially expressed genes and differential splicing events were analyzed.Finally,the genes responded to cold stress in Arabidopsis genome were detected.This work is helpful for elucidating the regulated mechanisms of gene expression and alternative splicing of tissue development and seed germination in plant genome.It will also provide a guideline for the understanding of gene expression and alternative splicing under environmental stress.