This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research
Identification, evolution and alternative splicing profile analysis of Serine/Arginine-Rich Protein Splicing Factors (SR Proteins) in poplar, Arabidopsis, grape, and papaya
Yan Xiang
Anhui Agricultural University
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
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.
Keywords
Intron retaining, Serine/Arginine-Rich, abiotic stresses, alternative splicing, gene duplication
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
This is a list of supplementary files associated with this preprint. Click to download.
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 30 Dec, 2019
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Plant Molecular Biology and Genetics
Learn more about our company.
This is a preprint. It has not completed peer review.
Research
Identification, evolution and alternative splicing profile analysis of Serine/Arginine-Rich Protein Splicing Factors (SR Proteins) in poplar, Arabidopsis, grape, and papaya
Yan Xiang
Anhui Agricultural University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 30 Dec, 2019
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Plant Molecular Biology and Genetics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
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.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8