Major Findings:
• Standardized methodologies, termed as miRPreM and tiRPreM, for the prediction of miRNAs and tRFs, respectively:
• Organism-specific reference genome • Presence in all the replicates • Normalized read count support • Perfect match search • At least two tools with multiple runs for high-confidence prediction
• Demonstrated :
• The existence of species-specific miRNAs
• Enhanced number of miRNAs (from published chickpea data)
• Prediction of tRFs from the sRNA data previously used for miRNA prediction only
Outcomes:
• First ever genome-specific study for the identification and analysis of miRNAs, tRFs and circRNAs under salinity stress
• First ever comparative study of miRNAs and tRFs from contrasting rice genotypes - IR29, Nonabokra and Oryza coarctata, under salinity stress at reproductive stage
• Significant number of DE miRNAs , tRFs and circRNAs
• Salt-stress related miRNA-mRNA-circRNA and tRF-mRNA-circRNA modules to investigate
• Significant number of salinity stress responsive genes from salt-sensitive and salt-tolerant rice cultivars
Publications:
1. Rawal, H.C., Ali, S., Mondal, T.K. miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms. Briefings in Bioinformatics. 23(1): bbab448b. doi: 10.1093/bib/bbab448 (2021).
2. Rawal, H.C., Ali, S., Mondal, T.K. Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs. International Journal of Biological Macromolecules. 242(3):125172. doi: 10.1016/j.ijbiomac.2023.125172. (2023).