Identification and characterization of long noncoding RNAs involved in the aluminum stress response in Medicago truncatula via genome-wide analysis
Numerous studies have shown that plant long noncoding RNAs (lncRNAs) play an important regulatory role in the plant response to environmental stress. However, there are no reports on lncRNAs regulating and enhancing aluminum (Al) stress tolerance in legumes. This study analyzed the role of lncRNAs i...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-09-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1017869/full |
| _version_ | 1798001416609988608 |
|---|---|
| author | Qihui Gui Qihui Gui Zhengyu Yang Chao Chen Chao Chen Feng Yang Song Wang Rui Dong Rui Dong |
| author_facet | Qihui Gui Qihui Gui Zhengyu Yang Chao Chen Chao Chen Feng Yang Song Wang Rui Dong Rui Dong |
| author_sort | Qihui Gui |
| collection | DOAJ |
| description | Numerous studies have shown that plant long noncoding RNAs (lncRNAs) play an important regulatory role in the plant response to environmental stress. However, there are no reports on lncRNAs regulating and enhancing aluminum (Al) stress tolerance in legumes. This study analyzed the role of lncRNAs in response to Al stress in the legume model plant Medicago truncatula. A total of 219.49 Gb clean data were generated: 3,284 lncRNA genes were identified, of which 515 were differentially expressed, and 1,254 new genes were functionally annotated through database alignment. We further predicted and classified putative targets of these lncRNAs and found that they were enriched in biological processes and metabolic pathways such as plant hormone signal transduction, cell wall modification and the tricarboxylic acid (TCA) cycle. Finally, we characterized the functions of 2 Al-activated-malate-transporter-related lncRNAs in yeast. The recombinant plasmids of MSTRG.12506.5 and MSTRG.34338.20 were transformed into yeast, and these yeast exhibited better growth than those carrying empty vectors on medium supplemented with 10 μM AlCl3 and showed that they have biological functions affording Al stress tolerance. These findings suggest that lncRNAs are involved in regulating plant responses to Al stress. Our findings help to understand the role of lncRNAs in the response to Al stress in legumes and provide candidate lncRNAs for further studies. |
| first_indexed | 2024-04-11T11:36:56Z |
| format | Article |
| id | doaj.art-97bfeb462318408f8b9a5322053a83ba |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T11:36:56Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-97bfeb462318408f8b9a5322053a83ba2022-12-22T04:25:57ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-09-011310.3389/fpls.2022.10178691017869Identification and characterization of long noncoding RNAs involved in the aluminum stress response in Medicago truncatula via genome-wide analysisQihui Gui0Qihui Gui1Zhengyu Yang2Chao Chen3Chao Chen4Feng Yang5Song Wang6Rui Dong7Rui Dong8Department of Grassland Science, College of Animal Science, Guizhou University, Guiyang, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, ChinaGuizhou Technological College of Machinery and Electricity, Duyun, ChinaDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, ChinaGrassland Technology Experiment and Extension Station, Guiyang, ChinaGrassland Technology Experiment and Extension Station, Guiyang, ChinaDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, ChinaNumerous studies have shown that plant long noncoding RNAs (lncRNAs) play an important regulatory role in the plant response to environmental stress. However, there are no reports on lncRNAs regulating and enhancing aluminum (Al) stress tolerance in legumes. This study analyzed the role of lncRNAs in response to Al stress in the legume model plant Medicago truncatula. A total of 219.49 Gb clean data were generated: 3,284 lncRNA genes were identified, of which 515 were differentially expressed, and 1,254 new genes were functionally annotated through database alignment. We further predicted and classified putative targets of these lncRNAs and found that they were enriched in biological processes and metabolic pathways such as plant hormone signal transduction, cell wall modification and the tricarboxylic acid (TCA) cycle. Finally, we characterized the functions of 2 Al-activated-malate-transporter-related lncRNAs in yeast. The recombinant plasmids of MSTRG.12506.5 and MSTRG.34338.20 were transformed into yeast, and these yeast exhibited better growth than those carrying empty vectors on medium supplemented with 10 μM AlCl3 and showed that they have biological functions affording Al stress tolerance. These findings suggest that lncRNAs are involved in regulating plant responses to Al stress. Our findings help to understand the role of lncRNAs in the response to Al stress in legumes and provide candidate lncRNAs for further studies.https://www.frontiersin.org/articles/10.3389/fpls.2022.1017869/fulllong noncoding RNAMedicago truncatulaaluminum stressmolecular regulatory mechanismhigh-throughput sequencing |
| spellingShingle | Qihui Gui Qihui Gui Zhengyu Yang Chao Chen Chao Chen Feng Yang Song Wang Rui Dong Rui Dong Identification and characterization of long noncoding RNAs involved in the aluminum stress response in Medicago truncatula via genome-wide analysis Frontiers in Plant Science long noncoding RNA Medicago truncatula aluminum stress molecular regulatory mechanism high-throughput sequencing |
| title | Identification and characterization of long noncoding RNAs involved in the aluminum stress response in Medicago truncatula via genome-wide analysis |
| title_full | Identification and characterization of long noncoding RNAs involved in the aluminum stress response in Medicago truncatula via genome-wide analysis |
| title_fullStr | Identification and characterization of long noncoding RNAs involved in the aluminum stress response in Medicago truncatula via genome-wide analysis |
| title_full_unstemmed | Identification and characterization of long noncoding RNAs involved in the aluminum stress response in Medicago truncatula via genome-wide analysis |
| title_short | Identification and characterization of long noncoding RNAs involved in the aluminum stress response in Medicago truncatula via genome-wide analysis |
| title_sort | identification and characterization of long noncoding rnas involved in the aluminum stress response in medicago truncatula via genome wide analysis |
| topic | long noncoding RNA Medicago truncatula aluminum stress molecular regulatory mechanism high-throughput sequencing |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1017869/full |
| work_keys_str_mv | AT qihuigui identificationandcharacterizationoflongnoncodingrnasinvolvedinthealuminumstressresponseinmedicagotruncatulaviagenomewideanalysis AT qihuigui identificationandcharacterizationoflongnoncodingrnasinvolvedinthealuminumstressresponseinmedicagotruncatulaviagenomewideanalysis AT zhengyuyang identificationandcharacterizationoflongnoncodingrnasinvolvedinthealuminumstressresponseinmedicagotruncatulaviagenomewideanalysis AT chaochen identificationandcharacterizationoflongnoncodingrnasinvolvedinthealuminumstressresponseinmedicagotruncatulaviagenomewideanalysis AT chaochen identificationandcharacterizationoflongnoncodingrnasinvolvedinthealuminumstressresponseinmedicagotruncatulaviagenomewideanalysis AT fengyang identificationandcharacterizationoflongnoncodingrnasinvolvedinthealuminumstressresponseinmedicagotruncatulaviagenomewideanalysis AT songwang identificationandcharacterizationoflongnoncodingrnasinvolvedinthealuminumstressresponseinmedicagotruncatulaviagenomewideanalysis AT ruidong identificationandcharacterizationoflongnoncodingrnasinvolvedinthealuminumstressresponseinmedicagotruncatulaviagenomewideanalysis AT ruidong identificationandcharacterizationoflongnoncodingrnasinvolvedinthealuminumstressresponseinmedicagotruncatulaviagenomewideanalysis |