Identification of long non-coding RNAs in response to downy mildew stress in grape
The importance of long non-coding RNA in plants has been reported more frequently in recent years, but there has been few specific reports on lncRNAs in grape, especially in terms of disease resistance. We performed RNA-seq on grape leaves of two species (Vitis piasezkii accession Liuba-8, Vitis vin...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Maximum Academic Press
2022-01-01
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| Series: | Fruit Research |
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| Online Access: | https://www.maxapress.com/article/doi/10.48130/FruRes-2022-0019 |
| _version_ | 1797293140104708096 |
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| author | Meijie Li Mengru Dou Ruiqi Liu Yuntong Jiao Zhiqiang Hao Yan Xu |
| author_facet | Meijie Li Mengru Dou Ruiqi Liu Yuntong Jiao Zhiqiang Hao Yan Xu |
| author_sort | Meijie Li |
| collection | DOAJ |
| description | The importance of long non-coding RNA in plants has been reported more frequently in recent years, but there has been few specific reports on lncRNAs in grape, especially in terms of disease resistance. We performed RNA-seq on grape leaves of two species (Vitis piasezkii accession Liuba-8, Vitis vinifera cultivar Pinot Noir) sampled at six time points after inoculation, and 4011 possible lncRNAs were identified. The characteristics of grape lncRNAs were analyzed, and it was found that lncRNAs showed relatively consistent characteristics with the reported lncRNAs in model plants. 3,643 lncRNAs were predicted that have cis-regulatory effects on 6,622 protein-coding genes and 91 DElncRNAs were revealed to be coexpressed with its trans-regulated coding genes. One hundred and seventeen grape microRNAs were predicted to potentially target 184 lncRNAs and six lncRNAs were predicted to be endogenous targeting mimics of 15 microRNAs, among which some miRNAs have been reported in grape disease resistance. At six time points, LncRNAs showed different expression levels and different expression patterns in two species, suggesting that lncRNAs may have a certain regulatory effect on resistance to downy mildew in grape. Finally, a lncRNA MSTRG.12742.1 which may play a positive role in grape downy mildew resistance was verified by transient transformation. Its potential target gene, VIT_204s0008g02671.1, encodes cryptochrome DASH which may regulate stomatal opening and closing of plant leaves. In this study, we provided the systematic identification of lncRNAs in the course of downy mildew of grape, laying a foundation for further studies on downy mildew and lncRNAs of grape in the future. |
| first_indexed | 2024-03-07T20:08:34Z |
| format | Article |
| id | doaj.art-07363043ff4348618a19f8b14e79152c |
| institution | Directory Open Access Journal |
| issn | 2769-4615 |
| language | English |
| last_indexed | 2024-03-07T20:08:34Z |
| publishDate | 2022-01-01 |
| publisher | Maximum Academic Press |
| record_format | Article |
| series | Fruit Research |
| spelling | doaj.art-07363043ff4348618a19f8b14e79152c2024-02-28T03:19:34ZengMaximum Academic PressFruit Research2769-46152022-01-012111410.48130/FruRes-2022-0019FruRes-2022-0019Identification of long non-coding RNAs in response to downy mildew stress in grapeMeijie Li0Mengru Dou1Ruiqi Liu2Yuntong Jiao3Zhiqiang Hao4Yan Xu5State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, ChinaCollege of Life Sciences, Shaanxi Normal University, Xi'an 710119, ChinaState Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, ChinaThe importance of long non-coding RNA in plants has been reported more frequently in recent years, but there has been few specific reports on lncRNAs in grape, especially in terms of disease resistance. We performed RNA-seq on grape leaves of two species (Vitis piasezkii accession Liuba-8, Vitis vinifera cultivar Pinot Noir) sampled at six time points after inoculation, and 4011 possible lncRNAs were identified. The characteristics of grape lncRNAs were analyzed, and it was found that lncRNAs showed relatively consistent characteristics with the reported lncRNAs in model plants. 3,643 lncRNAs were predicted that have cis-regulatory effects on 6,622 protein-coding genes and 91 DElncRNAs were revealed to be coexpressed with its trans-regulated coding genes. One hundred and seventeen grape microRNAs were predicted to potentially target 184 lncRNAs and six lncRNAs were predicted to be endogenous targeting mimics of 15 microRNAs, among which some miRNAs have been reported in grape disease resistance. At six time points, LncRNAs showed different expression levels and different expression patterns in two species, suggesting that lncRNAs may have a certain regulatory effect on resistance to downy mildew in grape. Finally, a lncRNA MSTRG.12742.1 which may play a positive role in grape downy mildew resistance was verified by transient transformation. Its potential target gene, VIT_204s0008g02671.1, encodes cryptochrome DASH which may regulate stomatal opening and closing of plant leaves. In this study, we provided the systematic identification of lncRNAs in the course of downy mildew of grape, laying a foundation for further studies on downy mildew and lncRNAs of grape in the future.https://www.maxapress.com/article/doi/10.48130/FruRes-2022-0019downy mildewlong non-coding rnasrnaseqgrape |
| spellingShingle | Meijie Li Mengru Dou Ruiqi Liu Yuntong Jiao Zhiqiang Hao Yan Xu Identification of long non-coding RNAs in response to downy mildew stress in grape Fruit Research downy mildew long non-coding rnas rnaseq grape |
| title | Identification of long non-coding RNAs in response to downy mildew stress in grape |
| title_full | Identification of long non-coding RNAs in response to downy mildew stress in grape |
| title_fullStr | Identification of long non-coding RNAs in response to downy mildew stress in grape |
| title_full_unstemmed | Identification of long non-coding RNAs in response to downy mildew stress in grape |
| title_short | Identification of long non-coding RNAs in response to downy mildew stress in grape |
| title_sort | identification of long non coding rnas in response to downy mildew stress in grape |
| topic | downy mildew long non-coding rnas rnaseq grape |
| url | https://www.maxapress.com/article/doi/10.48130/FruRes-2022-0019 |
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