Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysis
As important regulators of alternative splicing (AS) events, serine/arginine (SR)-rich proteins play indispensable roles in the growth and development of organisms. Until now, the study of SR genes has been lacking in plants. In the current study, we performed genome-wide analysis on the SR gene fam...
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PeerJ Inc.
2023-10-01
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| author | Rui Gao Yingying Lu Nan Wu Hui Liu Xiaoli Jin |
| author_facet | Rui Gao Yingying Lu Nan Wu Hui Liu Xiaoli Jin |
| author_sort | Rui Gao |
| collection | DOAJ |
| description | As important regulators of alternative splicing (AS) events, serine/arginine (SR)-rich proteins play indispensable roles in the growth and development of organisms. Until now, the study of SR genes has been lacking in plants. In the current study, we performed genome-wide analysis on the SR gene family in rice. A total of 24 OsSR genes were phylogenetically classified into seven groups, corresponding to seven subfamilies. The OsSR genes’ structures, distribution of conserved domains, and protein tertiary structure of OsSR were conserved within each subfamily. The synteny analysis revealed that segmental duplication events were critical for the expansion of OsSR gene family. Moreover, interspecific synteny revealed the distribution of orthologous SR gene pairs between rice and Arabidopsis, sorghum, wheat, and maize. Among all OsSR genes, 14 genes exhibited NAGNAG acceptors, and only four OsSR genes had AS events on the NAGNAG acceptors. Furthermore, the distinct tissue-specific expression patterns of OsSR genes showed that these genes may function in different developmental stages in rice. The AS patterns on the same OsSR gene were variable among the root, stem, leaf, and grains at different filling stages, and some isoforms could only be detected in one or a few of tested tissues. Meanwhile, our results showed that the expression of some OsSR genes changed dramatically under ABA, GA, salt, drought, cold or heat treatment, which were related to the wide distribution of corresponding cis-elements in their promoter regions, suggesting their specific roles in stress and hormone response. This research facilitates our understanding of SR gene family in rice and provides clues for further exploration of the function of OsSR genes. |
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| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T03:56:32Z |
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| spelling | doaj.art-651db7829ef54e19badd21f87c0a92652023-12-03T14:20:16ZengPeerJ Inc.PeerJ2167-83592023-10-0111e1619310.7717/peerj.16193Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysisRui Gao0Yingying Lu1Nan Wu2Hui Liu3Xiaoli Jin4Department of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, ChinaDepartment of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, ChinaDepartment of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, ChinaDepartment of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, ChinaDepartment of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, ChinaAs important regulators of alternative splicing (AS) events, serine/arginine (SR)-rich proteins play indispensable roles in the growth and development of organisms. Until now, the study of SR genes has been lacking in plants. In the current study, we performed genome-wide analysis on the SR gene family in rice. A total of 24 OsSR genes were phylogenetically classified into seven groups, corresponding to seven subfamilies. The OsSR genes’ structures, distribution of conserved domains, and protein tertiary structure of OsSR were conserved within each subfamily. The synteny analysis revealed that segmental duplication events were critical for the expansion of OsSR gene family. Moreover, interspecific synteny revealed the distribution of orthologous SR gene pairs between rice and Arabidopsis, sorghum, wheat, and maize. Among all OsSR genes, 14 genes exhibited NAGNAG acceptors, and only four OsSR genes had AS events on the NAGNAG acceptors. Furthermore, the distinct tissue-specific expression patterns of OsSR genes showed that these genes may function in different developmental stages in rice. The AS patterns on the same OsSR gene were variable among the root, stem, leaf, and grains at different filling stages, and some isoforms could only be detected in one or a few of tested tissues. Meanwhile, our results showed that the expression of some OsSR genes changed dramatically under ABA, GA, salt, drought, cold or heat treatment, which were related to the wide distribution of corresponding cis-elements in their promoter regions, suggesting their specific roles in stress and hormone response. This research facilitates our understanding of SR gene family in rice and provides clues for further exploration of the function of OsSR genes.https://peerj.com/articles/16193.pdfRice (Oryza sativa L.)OsSR genesAlternative splicingExpression profileAbiotic stress |
| spellingShingle | Rui Gao Yingying Lu Nan Wu Hui Liu Xiaoli Jin Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysis PeerJ Rice (Oryza sativa L.) OsSR genes Alternative splicing Expression profile Abiotic stress |
| title | Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysis |
| title_full | Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysis |
| title_fullStr | Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysis |
| title_full_unstemmed | Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysis |
| title_short | Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysis |
| title_sort | comprehensive study of serine arginine rich sr gene family in rice characterization evolution and expression analysis |
| topic | Rice (Oryza sativa L.) OsSR genes Alternative splicing Expression profile Abiotic stress |
| url | https://peerj.com/articles/16193.pdf |
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