Genome-wide Survey Of Alternative Splicing In Several Kinds Of Economic Plants

Alternative splicing plays a major role in the diversification of gene function and regulation. Therefore, the identification and analysis of transient regulation of alternative splicing isoforms generated by the system will help control the growth of crops and traits. We had identified thousands of alternative splicing events using High-throughput transcriptome sequencing data of different tissue samples in different stages. We hope to find the alternative splicing pattern and regulation pathways of plant gene expression which Alternative splicing involved in. In this study, RNA-seq data from different organs(leaf, immature fruit, mature fruit and half-ripe fruit) of Actinidia chinensis had been used to identify the alternative splicing events using the A. chinensis genome as reference, while taking advantage of RNA-seq data from five organs(seed, root, stem, Floral Bud, leaf and apical meristem after 0-4 short days) of Glycine max had been used to identify the alternative splicing events using the G. max genome as reference. Combined with the genomic analysis of alternative splicing of Brassica rapa and Brassica oleracea to do the multi-species research of alternative splicing. The results are as follows:1. 32180 alternative splicing events were discovered from the A. chinensis genome corresponding to 11651 genes(29% of the total genome) had been found.117927 alternative splicing events was discovered from the G. max genome corresponding to 24826 genes(45.8% of the total genome) had been found. Intron retention occurs most frequently in diverse types of alternative splicing(about 60%).The frequency of events with alternative 3' splice sites was twice than the alternative5' splice sites.2. The alternative splicing events in different organs of A. chinensis seemed to preferentially occurred in genes with important function. Genes of leaf are associated with the function of actin and microtubule. Genes of immature fruit decided the function of two-component signal system.Genes of half-ripe fruit are connected with phospholipid synthesis process. Genes in mature fruit associated with signal transduction. Genes of G. max root is associated with antioxidant and peroxidase.Genes of G. max stem are associated with the cell wall. Genes of G. max seeds are combined with material synthesis.3. 55.6% of vitamin related genes had been found alternative splicing changes,which were significantly higher than the average changes of the genome(the average splicing change level was 29.6%).4. Alternative splicing participates in the expression of transcription factors in G.max. Transcription factors in different tissues have dissimilar Alternative splicing events. The difference between alternative splicing events of transcription factors in differents period becomes smaller as the tissue matures.5. We found out the genes observed alternative splicing events in both four species and done the singular enrichment analysis. It has been found that alternative splicing events involved in the regulation of most of the physiological pathways, and these genes play an important role in the cell membrane properties, organelles and membrane-bounded organelle, its main function are binding, location and catalysis.