Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress
Plants must reprogram gene expression to adapt constantly changing environmental temperatures. With the increased occurrence of extremely low temperatures, the negative effects on plants, especially on growth and development, from cold stress are becoming more and more serious. In this research, str...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-08-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.983460/full |
| _version_ | 1811188707094429696 |
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| author | Yue Liu Yue Liu Yajun Cai Yajun Cai Yanzhuo Li Yanzhuo Li Xiaoling Zhang Xiaoling Zhang Nan Shi Nan Shi Jingze Zhao Jingze Zhao Hongchun Yang Hongchun Yang Hongchun Yang |
| author_facet | Yue Liu Yue Liu Yajun Cai Yajun Cai Yanzhuo Li Yanzhuo Li Xiaoling Zhang Xiaoling Zhang Nan Shi Nan Shi Jingze Zhao Jingze Zhao Hongchun Yang Hongchun Yang Hongchun Yang |
| author_sort | Yue Liu |
| collection | DOAJ |
| description | Plants must reprogram gene expression to adapt constantly changing environmental temperatures. With the increased occurrence of extremely low temperatures, the negative effects on plants, especially on growth and development, from cold stress are becoming more and more serious. In this research, strand-specific RNA sequencing (ssRNA-seq) was used to explore the dynamic changes in the transcriptome landscape of Arabidopsis thaliana exposed to cold temperatures (4°C) at different times. In total, 7,623 differentially expressed genes (DEGs) exhibited dynamic temporal changes during the cold treatments. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were enriched in cold response, secondary metabolic processes, photosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction pathways. Meanwhile, long non-coding RNAs (lncRNAs) were identified after the assembly of the transcripts, from which 247 differentially expressed lncRNAs (DElncRNAs) and their potential target genes were predicted. 3,621 differentially alternatively spliced (DAS) genes related to RNA splicing and spliceosome were identified, indicating enhanced transcriptome complexity due to the alternative splicing (AS) in the cold. In addition, 739 cold-regulated transcription factors (TFs) belonging to 52 gene families were identified as well. This research analyzed the dynamic changes of the transcriptome landscape in response to cold stress, which reveals more complete transcriptional patterns during short- and long-term cold treatment and provides new insights into functional studies of that how plants are affected by cold stress. |
| first_indexed | 2024-04-11T14:24:01Z |
| format | Article |
| id | doaj.art-12cb496748584d2b8694ab6809ad4fdd |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T14:24:01Z |
| publishDate | 2022-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-12cb496748584d2b8694ab6809ad4fdd2022-12-22T04:18:56ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-08-011310.3389/fpls.2022.983460983460Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stressYue Liu0Yue Liu1Yajun Cai2Yajun Cai3Yanzhuo Li4Yanzhuo Li5Xiaoling Zhang6Xiaoling Zhang7Nan Shi8Nan Shi9Jingze Zhao10Jingze Zhao11Hongchun Yang12Hongchun Yang13Hongchun Yang14State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaHubei Hongshan Laboratory, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaHubei Hongshan Laboratory, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaHubei Hongshan Laboratory, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaHubei Hongshan Laboratory, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaHubei Hongshan Laboratory, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaHubei Hongshan Laboratory, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaHubei Hongshan Laboratory, Wuhan, ChinaRNA Institute, Wuhan University, Wuhan, ChinaPlants must reprogram gene expression to adapt constantly changing environmental temperatures. With the increased occurrence of extremely low temperatures, the negative effects on plants, especially on growth and development, from cold stress are becoming more and more serious. In this research, strand-specific RNA sequencing (ssRNA-seq) was used to explore the dynamic changes in the transcriptome landscape of Arabidopsis thaliana exposed to cold temperatures (4°C) at different times. In total, 7,623 differentially expressed genes (DEGs) exhibited dynamic temporal changes during the cold treatments. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were enriched in cold response, secondary metabolic processes, photosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction pathways. Meanwhile, long non-coding RNAs (lncRNAs) were identified after the assembly of the transcripts, from which 247 differentially expressed lncRNAs (DElncRNAs) and their potential target genes were predicted. 3,621 differentially alternatively spliced (DAS) genes related to RNA splicing and spliceosome were identified, indicating enhanced transcriptome complexity due to the alternative splicing (AS) in the cold. In addition, 739 cold-regulated transcription factors (TFs) belonging to 52 gene families were identified as well. This research analyzed the dynamic changes of the transcriptome landscape in response to cold stress, which reveals more complete transcriptional patterns during short- and long-term cold treatment and provides new insights into functional studies of that how plants are affected by cold stress.https://www.frontiersin.org/articles/10.3389/fpls.2022.983460/fullArabidopsis thalianacold stressssRNA-seqtranscriptome landscapedynamic changelong non-coding RNA |
| spellingShingle | Yue Liu Yue Liu Yajun Cai Yajun Cai Yanzhuo Li Yanzhuo Li Xiaoling Zhang Xiaoling Zhang Nan Shi Nan Shi Jingze Zhao Jingze Zhao Hongchun Yang Hongchun Yang Hongchun Yang Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress Frontiers in Plant Science Arabidopsis thaliana cold stress ssRNA-seq transcriptome landscape dynamic change long non-coding RNA |
| title | Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress |
| title_full | Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress |
| title_fullStr | Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress |
| title_full_unstemmed | Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress |
| title_short | Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress |
| title_sort | dynamic changes in the transcriptome landscape of arabidopsis thaliana in response to cold stress |
| topic | Arabidopsis thaliana cold stress ssRNA-seq transcriptome landscape dynamic change long non-coding RNA |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.983460/full |
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