Genome-Wide Identification of Long Non-Coding RNAs in Pearl Millet (<i>Pennisetum glaucum</i> (L.)) Genotype Subjected to Drought Stress
Pearl millet (<i>Pennisetum glaucum</i> L.) is affected by drought stress, affecting crop productivity and survival. Long non-coding RNAs (lncRNAs) are reported to play a vital role in the response to drought stress. LncRNAs represent a major part of non-protein coding RNAs and are prese...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-08-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/12/8/1976 |
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| author | Baibhav Kumar Animesh Kumar Sarika Jaiswal Mir Asif Iquebal Ulavappa B. Angadi Rukam S. Tomar Anil Rai Dinesh Kumar |
| author_facet | Baibhav Kumar Animesh Kumar Sarika Jaiswal Mir Asif Iquebal Ulavappa B. Angadi Rukam S. Tomar Anil Rai Dinesh Kumar |
| author_sort | Baibhav Kumar |
| collection | DOAJ |
| description | Pearl millet (<i>Pennisetum glaucum</i> L.) is affected by drought stress, affecting crop productivity and survival. Long non-coding RNAs (lncRNAs) are reported to play a vital role in the response to drought stress. LncRNAs represent a major part of non-protein coding RNAs and are present prevalently. These are involved in various biological processes, which may functionally act as RNA rather than getting transcribed as protein. We targeted genome-wide identification of lncRNAs in pearl millet from root and leaf tissues subjected to drought stress. A total of 879 lncRNAs were identified, out of which 209 (leaf control, root control), 198 (leaf treated, root treated), 115 (leaf control, leaf treated) and 194 (root control, root treated) were differentially expressed. Two lncRNAs were found as potential target mimics of three miRNAs from the miRBase database. Gene ontology study revealed that drought-responsive lncRNAs are involved in biological processes like ‘metabolic process’ and ‘cellular process’, molecular functions like ‘binding’ and ‘catalytic activities’ and cellular components like ‘cell’, ‘cell part’ and ‘membrane part’. LncRNA-miRNA-mRNA network shows that it plays a vital role in the stress-responsive mechanism through their activities in hormone signal transduction, response to stress, response to auxin and transcription factor activity. Only four lncRNAs were found to get a match with the lncRNAs present in the plant lncRNA database CANTATAdb, which shows its poorly conserved nature among species. This information has been cataloged in the pearl millet drought-responsive long non-coding RNA database (PMDlncRDB). The discovered lncRNAs can be used in the improvement of important traits, as well as CISPR-Cas technology, in the editing of ncRNAs in plants for trait improvement. Such a study will increase our understanding of the expression behavior of lncRNAs, as well as its underlying mechanisms under drought stress in pearl millet. |
| first_indexed | 2024-03-09T04:48:50Z |
| format | Article |
| id | doaj.art-6073cf76e74044e7a637ec632f149da6 |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-09T04:48:50Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-6073cf76e74044e7a637ec632f149da62023-12-03T13:12:51ZengMDPI AGAgronomy2073-43952022-08-01128197610.3390/agronomy12081976Genome-Wide Identification of Long Non-Coding RNAs in Pearl Millet (<i>Pennisetum glaucum</i> (L.)) Genotype Subjected to Drought StressBaibhav Kumar0Animesh Kumar1Sarika Jaiswal2Mir Asif Iquebal3Ulavappa B. Angadi4Rukam S. Tomar5Anil Rai6Dinesh Kumar7Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, IndiaDivision of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, IndiaDivision of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, IndiaDivision of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, IndiaDivision of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, IndiaDepartment of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh 362001, IndiaDivision of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, IndiaDivision of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, IndiaPearl millet (<i>Pennisetum glaucum</i> L.) is affected by drought stress, affecting crop productivity and survival. Long non-coding RNAs (lncRNAs) are reported to play a vital role in the response to drought stress. LncRNAs represent a major part of non-protein coding RNAs and are present prevalently. These are involved in various biological processes, which may functionally act as RNA rather than getting transcribed as protein. We targeted genome-wide identification of lncRNAs in pearl millet from root and leaf tissues subjected to drought stress. A total of 879 lncRNAs were identified, out of which 209 (leaf control, root control), 198 (leaf treated, root treated), 115 (leaf control, leaf treated) and 194 (root control, root treated) were differentially expressed. Two lncRNAs were found as potential target mimics of three miRNAs from the miRBase database. Gene ontology study revealed that drought-responsive lncRNAs are involved in biological processes like ‘metabolic process’ and ‘cellular process’, molecular functions like ‘binding’ and ‘catalytic activities’ and cellular components like ‘cell’, ‘cell part’ and ‘membrane part’. LncRNA-miRNA-mRNA network shows that it plays a vital role in the stress-responsive mechanism through their activities in hormone signal transduction, response to stress, response to auxin and transcription factor activity. Only four lncRNAs were found to get a match with the lncRNAs present in the plant lncRNA database CANTATAdb, which shows its poorly conserved nature among species. This information has been cataloged in the pearl millet drought-responsive long non-coding RNA database (PMDlncRDB). The discovered lncRNAs can be used in the improvement of important traits, as well as CISPR-Cas technology, in the editing of ncRNAs in plants for trait improvement. Such a study will increase our understanding of the expression behavior of lncRNAs, as well as its underlying mechanisms under drought stress in pearl millet.https://www.mdpi.com/2073-4395/12/8/1976lncRNAspearl milletdroughtmiRNAsweb resource |
| spellingShingle | Baibhav Kumar Animesh Kumar Sarika Jaiswal Mir Asif Iquebal Ulavappa B. Angadi Rukam S. Tomar Anil Rai Dinesh Kumar Genome-Wide Identification of Long Non-Coding RNAs in Pearl Millet (<i>Pennisetum glaucum</i> (L.)) Genotype Subjected to Drought Stress Agronomy lncRNAs pearl millet drought miRNAs web resource |
| title | Genome-Wide Identification of Long Non-Coding RNAs in Pearl Millet (<i>Pennisetum glaucum</i> (L.)) Genotype Subjected to Drought Stress |
| title_full | Genome-Wide Identification of Long Non-Coding RNAs in Pearl Millet (<i>Pennisetum glaucum</i> (L.)) Genotype Subjected to Drought Stress |
| title_fullStr | Genome-Wide Identification of Long Non-Coding RNAs in Pearl Millet (<i>Pennisetum glaucum</i> (L.)) Genotype Subjected to Drought Stress |
| title_full_unstemmed | Genome-Wide Identification of Long Non-Coding RNAs in Pearl Millet (<i>Pennisetum glaucum</i> (L.)) Genotype Subjected to Drought Stress |
| title_short | Genome-Wide Identification of Long Non-Coding RNAs in Pearl Millet (<i>Pennisetum glaucum</i> (L.)) Genotype Subjected to Drought Stress |
| title_sort | genome wide identification of long non coding rnas in pearl millet i pennisetum glaucum i l genotype subjected to drought stress |
| topic | lncRNAs pearl millet drought miRNAs web resource |
| url | https://www.mdpi.com/2073-4395/12/8/1976 |
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