Identification, evolution and alternative splicing profile analysis of Serine/Arginine-Rich Protein Splicing Factors (SR Proteins) in poplar, Arabidopsis, grape, and papaya

Alternative splicing (AS) regulates gene expression and produces proteome diversity. Serine/Arginine-Rich Protein Splicing Factors (SR Proteins) are important splicing factors that play significant roles in spliceosome assembly and splicing regulation, and play roles in regulating plant stress. In this report, we analyzed 30 SR genes in Populus trichocarpa, 18 genes in Arabidopsis thaliana, 14 genes in Vitis vinifera and 9 genes in Carica papaya. The SR proteins contained RRM and RS conserved domains, and based on different structural domain organization were divided into six subfamilies (SR, SC, SCL, RS, RSZ and RS2Z). Gene duplication analysis revealed 94 paralogs and 408 orthologs in the four species, and the SR genes had undergone strong purifying selection. A number of stress-related cis-elements (ABRE, LTR, MBS, TC-rich repeats cis-acting element) were identified in the promoters of the SR genes. Microarray and RNA-seq data showed that SR genes expression in different tissues of the four species responded differently to abiotic stress. Poplar, Arabidopsis and grape SR genes had many splice isoforms. Moreover, 26 of 30 poplar SR genes had intron retention (IR) events, and the relative IR rates of 27 intron sites in the poplar SR genes changed significantly under cold, heat, drought and salt stress conditions. This study provides valuable resources for the gene structure, function, and evolution of poplar SR proteins.