Comparative miRNAome Analysis Revealed Numerous Conserved and Novel Drought Responsive miRNAs in Cotton (Gossypium spp.)
1 Department of Plant Molecular Biology and Bioinformatics, Center for Plant Molecular Biology and Biotechnology, India
2 Department of Fruit Crops, Horticultural College and Research Institute, TNAU, Periyakulam, 625604, India
3 Department of Millets, CPBG, Tamil Nadu Agricultural University (TNAU), Coimbatore, 641003, India
Cotton Genomics and Genetics, 2016, Vol. 7, No. 2 doi: 10.5376/cgg.2016.07.0002
Received: 15 Apr., 2016 Accepted: 15 May, 2016 Published: 19 May, 2016
© 2016 BioPublisher Publishing Platform
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Preferred citation for this article:
Boopathi M.N., Sathish S., Kavitha P., Dachinamoorthy P, and Ravikesavan R., 2016, Comparative miRNAome Analysis Revealed Numerous Conserved and Novel Drought Responsive miRNAs in Cotton (Gossypium spp.), Cotton Genomics and Genetics, 7(2): 1-23 (doi: 10.5376/cgg.2016.07.0002)
Negative regulations of gene expression by endogenous, non-coding miRNAs have been shown to play important role in abiotic stress responses in plants. However, limited knowledge is available on water stress responsive miRNAs in cotton. In this study, differentially expressed drought responsive miRNAs and their targets were identified under natural field conditions through high-throughput small RNA sequencing by comparing leaf samples of drought tolerant Gossypium hirsutum cv. KC3 and drought susceptible G. barbadense cv. Suvin. Totally four small RNA libraries were constructed and sequenced by employing ion protonTM technology. Altogether, there were 39 407 089 reads with a mean read length of 22 nt. In KC3, there were 5 138 unique miRNA reads that were differentially expressed with at least two folds under water stressed conditions. In contrast, Suvin have shown 8 469 unique miRNA reads that were differentially expressed with minimum of two folds under water stressed conditions. Comparison of miRNAs expressed under water stressed conditions between KC3 and Suvin, have resulted 7 494 miRNA reads and interestingly majority of them were down regulated with at least two folds. Besides identifying large numbers of novel miRNAs, several abiotic stress responsive conserved miRNAs were also noticed. Of particular interest were miR750, miR2, miR14, miR276, miR279, miR-bantam and miR5176 that were highly down regulated in KC3 under water stress conditions. Strikingly, miR2 and miR-bantam were previously shown to target pre-apoptotic genes in biological systems. Further, the identified miRNAs were also targeting different classes of dehydrogenases, protein kinases and transcription factors. Our results revealed for the first time that there were large numbers of water stress related miRNAs that might be sequentially and/or complexly involved in gene regulation that confers drought tolerance in cotton under field conditions and they have enormous potential in elucidating the molecular mechanism of miRNA based gene regulation and more importantly in genetic improvement of drought tolerance in cotton. Further, this is the first report on experimentally identifying miRNAs in G. barbadense.
Cotton; Drought tolerance; MicroRNAs; Next generation sequencing; Transcriptomics