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Yu H, Bi X, Li Z, Fu X, Li Y, Li Y, Yang Y, Liu D, Li G, Dong W, Hu F. Transcriptomic Analysis of Alternative Splicing Events during Different Fruit Ripening Stages of Coffea arabica L. Genes (Basel) 2024; 15:459. [PMID: 38674393 PMCID: PMC11050144 DOI: 10.3390/genes15040459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
To date, genomic and transcriptomic data on Coffea arabica L. in public databases are very limited, and there has been no comprehensive integrated investigation conducted on alternative splicing (AS). Previously, we have constructed and sequenced eighteen RNA-seq libraries of C. arabica at different ripening stages of fruit development. From this dataset, a total of 3824, 2445, 2564, 2990, and 3162 DSGs were identified in a comparison of different fruit ripening stages. The largest proportion of DSGs, approximately 65%, were of the skipped exon (SE) type. Biologically, 9 and 29 differentially expressed DSGs in the spliceosome pathway and carbon metabolism pathway, respectively, were identified. These DSGs exhibited significant variations, primarily in S1 vs. S2 and S5 vs. S6, and they involve many aspects of organ development, hormone transduction, and the synthesis of flavor components. Through the examination of research findings regarding the biological functions and biochemical pathways associated with DSGs and DEGs, it was observed that six DSGs significantly enriched in ABC transporters, namely, LOC113712394, LOC113726618, LOC113739972, LOC113725240, LOC113730214, and LOC113707447, were continually down-regulated at the fruit ripening stage. In contrast, a total of four genes, which were LOC113732777, LOC113727880, LOC113690566, and LOC113711936, including those enriched in the cysteine and methionine metabolism, were continually up-regulated. Collectively, our findings may contribute to the exploration of alternative splicing mechanisms for focused investigations of potential genes associated with the ripening of fruits in C. arabica.
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Affiliation(s)
- Haohao Yu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Xiaofei Bi
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Zhongxian Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Xingfei Fu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Yanan Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Yaqi Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Yang Yang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Dexin Liu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Guiping Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Wenjiang Dong
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Faguang Hu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
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Han M, Niu M, Gao T, Shen Y, Zhou X, Zhang Y, Liu L, Chai M, Sun G, Wang Y. Responsive Alternative Splicing Events of Opisthopappus Species against Salt Stress. Int J Mol Sci 2024; 25:1227. [PMID: 38279226 PMCID: PMC10816081 DOI: 10.3390/ijms25021227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
Salt stress profoundly affects plant growth, prompting intricate molecular responses, such as alternative splicing (AS), for environmental adaptation. However, the response of AS events to salt stress in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear, which is a Taihang Mountain cliff-dwelling species. Using RNA-seq data, differentially expressed genes (DEGs) were identified under time and concentration gradients of salt stress. Two types of AS, skipped exon (SE) and mutually exclusive exons (MXE), were found. Differentially alternative splicing (DAS) genes in both species were significantly enriched in "protein phosphorylation", "starch and sucrose metabolism", and "plant hormone signal transduction" pathways. Meanwhile, distinct GO terms and KEGG pathways of DAS occurred between two species. Only a small subset of DAS genes overlapped with DEGs under salt stress. Although both species likely adopted protein phosphorylation to enhance salt stress tolerance, they exhibited distinct responses. The results indicated that the salt stress mechanisms of both Opisthopappus species exhibited similarities and differences in response to salt stress, which suggested that adaptive divergence might have occurred between them. This study initially provides a comprehensive description of salt responsive AS events in Opisthopappus and conveys some insights into the molecular mechanisms behind species tolerance on the Taihang Mountains.
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Affiliation(s)
- Mian Han
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Mengfan Niu
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Ting Gao
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Yuexin Shen
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Xiaojuan Zhou
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Yimeng Zhang
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Li Liu
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Min Chai
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Genlou Sun
- Department of Botany, Saint Mary’s University, Halifax, NS B3H 3C3, Canada
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
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Wei R, Zhang W, Li C, Hao Z, Huang D, Zhang W, Pan X. Establishment of Agrobacterium-mediated transformation system to Juglans sigillata Dode 'Qianhe-7'. Transgenic Res 2023; 32:193-207. [PMID: 37118332 DOI: 10.1007/s11248-023-00348-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 04/04/2023] [Indexed: 04/30/2023]
Abstract
An efficient genetic transformation system is of great significance for verifying gene function and improving plant breeding efficiency by gene engineering. In this study, a stable Agrobacterium mediated genetic transformation system of Juglans sigillata Dode 'Qianhe-7' was investigated using callus and negative pressure-assisted and ultrasonic-assisted transformation selection. The results showed that the axillary shoot leaves were suitable to induce callus and the callus proliferation rate could reach 516.27% when induction calli were cultured on DKW medium containing 0.5 mg L-1 indole-3-butyric acid, 1.2 mg L-1 2,4-dichlorophenoxyacetic acid and 0.5 mg L-1 kinetin for 18 d. In addition, negative pressure infection was the optimal infection method with the lowest browning rate (0.00%), high GFP conversion rate (16.67%), and better growth status. To further prove the feasibility of this genetic transformation system, the flavonol synthetase (JsFLS5) gene was successfully transformed into the into leaf-derived callus of 'Qianhe-7'. JsFLS5 expression and the content of total flavonoids in transformed callus were improved significantly compared with the untransformed callus, which proved that we had an efficient and reliable genetic transformation system using leaf-derived callus of Juglans sigillata.
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Affiliation(s)
- Rong Wei
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Wen'e Zhang
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Chunxiang Li
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Zhenkun Hao
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Dong Huang
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Wenlong Zhang
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Xuejun Pan
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China.
- College of Agricultural, Guizhou University, Guiyang, 550025, China.
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Wang L, Wang L, Tan M, Wang L, Zhao W, You J, Wang L, Yan X, Wang W. The pattern of alternative splicing and DNA methylation alteration and their interaction in linseed (Linum usitatissimum L.) response to repeated drought stresses. Biol Res 2023; 56:12. [PMID: 36922868 PMCID: PMC10018860 DOI: 10.1186/s40659-023-00424-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Drought stress has significantly hampered agricultural productivity worldwide and can also result in modifications to DNA methylation levels. However, the dynamics of DNA methylation and its association with the changes in gene transcription and alternative splicing (AS) under drought stress are unknown in linseed, which is frequently cultivated in arid and semiarid regions. RESULTS We analysed AS events and DNA methylation patterns in drought-tolerant (Z141) and drought-sensitive (NY-17) linseed under drought stress (DS) and repeated drought stress (RD) treatments. We found that the number of intron-retention (IR) and alternative 3' splice site (Alt3'SS) events were significantly higher in Z141 and NY-17 under drought stress. We found that the linseed response to the DS treatment was mainly regulated by transcription, while the response to the RD treatment was coregulated by transcription and AS. Whole genome-wide DNA methylation analysis revealed that drought stress caused an increase in the overall methylation level of linseed. Although we did not observe any correlation between differentially methylated genes (DMGs) and differentially spliced genes (DSGs) in this study, we found that the DSGs whose gene body region was hypermethylated in Z141 and hypomethylated in NY-17 were enriched in abiotic stress response Gene Ontology (GO) terms. This finding implies that gene body methylation plays an important role in AS regulation in some specific genes. CONCLUSION Our study is the first comprehensive genome-wide analysis of the relationship between linseed methylation changes and AS under drought and repeated drought stress. Our study revealed different interaction patterns between differentially expressed genes (DEGs) and DSGs under DS and RD treatments and differences between methylation and AS regulation in drought-tolerant and drought-sensitive linseed varieties. The findings will probably be of interest in the future. Our results provide interesting insights into the association between gene expression, AS, and DNA methylation in linseed under drought stress. Differences in these associations may account for the differences in linseed drought tolerance.
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Affiliation(s)
- Ling Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Lei Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Meilian Tan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Wei Zhao
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | | | - Xingchu Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Wei Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China.
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Zhou E, Wang G, Weng L, Li M, Xiao H. Comparative Analysis of Environment-Responsive Alternative Splicing in the Inflorescences of Cultivated and Wild Tomato Species. Int J Mol Sci 2022; 23:11585. [PMID: 36232886 DOI: 10.3390/ijms231911585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Cultivated tomato (Solanum lycopersicum) is bred for fruit production in optimized environments, in contrast to harsh environments where their ancestral relatives thrive. The process of domestication and breeding has profound impacts on the phenotypic plasticity of plant development and the stress response. Notably, the alternative splicing (AS) of precursor message RNA (pre-mRNA), which is one of the major factors contributing to transcriptome complexity, is responsive to developmental cues and environmental change. To determine a possible association between AS events and phenotypic plasticity, we investigated environment-responsive AS events in the inflorescences of cultivated tomato and its ancestral relatives S. pimpinellifolium. Despite that similar AS frequencies were detected in the cultivated tomato variety Moneymaker and two S. pimpinellifolium accessions under the same growth conditions, 528 genes including splicing factors showed differential splicing in the inflorescences of plants grown in open fields and plastic greenhouses in the Moneymaker variety. In contrast, the two S. pimpinellifolium accessions, LA1589 and LA1781, had 298 and 268 genes showing differential splicing, respectively. Moreover, seven heat responsive genes showed opposite expression patterns in response to changing growth conditions between Moneymaker and its ancestral relatives. Accordingly, there were eight differentially expressed splice variants from genes involved in heat response in Moneymaker. Our results reveal distinctive features of AS events in the inflorescences between cultivated tomato and its ancestral relatives, and show that AS regulation in response to environmental changes is genotype dependent.
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