Identification of differentially expressed mungbean miRNAs and their targets in response to drought stress by small RNA deep sequencing
Abstractta: MicroRNAs (miRNAs) are small, non-coding RNAs, 18–25 nt in length, that play a crucial role in regulating genes associated with the physiological processes and responses to various biotic and abiotic stresses. Different conserved and species-specific microRNAs and their functions have be...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-06-01
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| Series: | Current Plant Biology |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2214662822000123 |
| _version_ | 1817977332400390144 |
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| author | Sanjeev Kumar Mahesh Das Ayan Sadhukhan Lingaraj Sahoo |
| author_facet | Sanjeev Kumar Mahesh Das Ayan Sadhukhan Lingaraj Sahoo |
| author_sort | Sanjeev Kumar |
| collection | DOAJ |
| description | Abstractta: MicroRNAs (miRNAs) are small, non-coding RNAs, 18–25 nt in length, that play a crucial role in regulating genes associated with the physiological processes and responses to various biotic and abiotic stresses. Different conserved and species-specific microRNAs and their functions have been identified, primarily in plants such as rice and Arabidopsis with sequenced genomes. Our present study identifies drought-responsive miRNAs and their potential targets from mungbean under three days of drought stress induced by PEG-6000. We constructed small RNA libraries from both control and drought-treated tolerant and susceptible mungbean genotypes and identified various miRNAs involved in drought stress regulation. Analysis of differentially expressed genes (DEGs) revealed 79 up-regulated and 158 down-regulated novel miRNAs and two up-and down-regulated known miRNAs under drought. Annotation of the miRNAs followed by target prediction and expression analysis revealed five miRNAs, Vra-miR160, Vra-miR164, Vra-miR167, Vra-miR394, and Vra-miR398, were potentially involved in the regulation of drought-responsive genes. Their predicted target genes were an Auxin response factor (ARF), a NAC (for petunia NAM and Arabidopsis ATAF1, ATAF2, and CUC2) transcription factor, Serine acetyltransferase 1, and Multicopper oxidase LPR2-like. The expression of drought-responsive miRNAs and their targets were validated by real-time PCR. Our data suggest that various known and novel microRNAs activated transcription factors, enzyme kinases, and hormone signaling pathways alleviate drought stress in the tolerant K-851 genotype of mungbean. |
| first_indexed | 2024-04-13T22:14:51Z |
| format | Article |
| id | doaj.art-ae74cf98265b43718e29389b4567b8fe |
| institution | Directory Open Access Journal |
| issn | 2214-6628 |
| language | English |
| last_indexed | 2024-04-13T22:14:51Z |
| publishDate | 2022-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Current Plant Biology |
| spelling | doaj.art-ae74cf98265b43718e29389b4567b8fe2022-12-22T02:27:35ZengElsevierCurrent Plant Biology2214-66282022-06-0130100246Identification of differentially expressed mungbean miRNAs and their targets in response to drought stress by small RNA deep sequencingSanjeev Kumar0Mahesh Das1Ayan Sadhukhan2Lingaraj Sahoo3Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India; Corresponding authors.Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, IndiaDepartment of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Rajasthan 342030, IndiaDepartment of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India; Corresponding authors.Abstractta: MicroRNAs (miRNAs) are small, non-coding RNAs, 18–25 nt in length, that play a crucial role in regulating genes associated with the physiological processes and responses to various biotic and abiotic stresses. Different conserved and species-specific microRNAs and their functions have been identified, primarily in plants such as rice and Arabidopsis with sequenced genomes. Our present study identifies drought-responsive miRNAs and their potential targets from mungbean under three days of drought stress induced by PEG-6000. We constructed small RNA libraries from both control and drought-treated tolerant and susceptible mungbean genotypes and identified various miRNAs involved in drought stress regulation. Analysis of differentially expressed genes (DEGs) revealed 79 up-regulated and 158 down-regulated novel miRNAs and two up-and down-regulated known miRNAs under drought. Annotation of the miRNAs followed by target prediction and expression analysis revealed five miRNAs, Vra-miR160, Vra-miR164, Vra-miR167, Vra-miR394, and Vra-miR398, were potentially involved in the regulation of drought-responsive genes. Their predicted target genes were an Auxin response factor (ARF), a NAC (for petunia NAM and Arabidopsis ATAF1, ATAF2, and CUC2) transcription factor, Serine acetyltransferase 1, and Multicopper oxidase LPR2-like. The expression of drought-responsive miRNAs and their targets were validated by real-time PCR. Our data suggest that various known and novel microRNAs activated transcription factors, enzyme kinases, and hormone signaling pathways alleviate drought stress in the tolerant K-851 genotype of mungbean.http://www.sciencedirect.com/science/article/pii/S2214662822000123Deep sequencingDifferentially expressed genesDroughtmicroRNAsMungbean |
| spellingShingle | Sanjeev Kumar Mahesh Das Ayan Sadhukhan Lingaraj Sahoo Identification of differentially expressed mungbean miRNAs and their targets in response to drought stress by small RNA deep sequencing Current Plant Biology Deep sequencing Differentially expressed genes Drought microRNAs Mungbean |
| title | Identification of differentially expressed mungbean miRNAs and their targets in response to drought stress by small RNA deep sequencing |
| title_full | Identification of differentially expressed mungbean miRNAs and their targets in response to drought stress by small RNA deep sequencing |
| title_fullStr | Identification of differentially expressed mungbean miRNAs and their targets in response to drought stress by small RNA deep sequencing |
| title_full_unstemmed | Identification of differentially expressed mungbean miRNAs and their targets in response to drought stress by small RNA deep sequencing |
| title_short | Identification of differentially expressed mungbean miRNAs and their targets in response to drought stress by small RNA deep sequencing |
| title_sort | identification of differentially expressed mungbean mirnas and their targets in response to drought stress by small rna deep sequencing |
| topic | Deep sequencing Differentially expressed genes Drought microRNAs Mungbean |
| url | http://www.sciencedirect.com/science/article/pii/S2214662822000123 |
| work_keys_str_mv | AT sanjeevkumar identificationofdifferentiallyexpressedmungbeanmirnasandtheirtargetsinresponsetodroughtstressbysmallrnadeepsequencing AT maheshdas identificationofdifferentiallyexpressedmungbeanmirnasandtheirtargetsinresponsetodroughtstressbysmallrnadeepsequencing AT ayansadhukhan identificationofdifferentiallyexpressedmungbeanmirnasandtheirtargetsinresponsetodroughtstressbysmallrnadeepsequencing AT lingarajsahoo identificationofdifferentiallyexpressedmungbeanmirnasandtheirtargetsinresponsetodroughtstressbysmallrnadeepsequencing |