Identification of conserved miRNAs and their targets in Jatropha curcas: an in silico approach

Foeaz Ahmed; Md Nazmul Islam Bappy; Md Shariful Islam

doi:10.1186/s43141-023-00495-9

Identification of conserved miRNAs and their targets in Jatropha curcas: an in silico approach

J Genet Eng Biotechnol. 2023 Apr 7;21(1):43. doi: 10.1186/s43141-023-00495-9.

Authors

Foeaz Ahmed^{1

2}, Md Nazmul Islam Bappy^{1

3}, Md Shariful Islam^{4

5}

Affiliations

¹ Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
² Department of Molecular Biology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
³ Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
⁴ Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh. sharif.mge@sau.ac.bd.
⁵ Department of Molecular Biology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh. sharif.mge@sau.ac.bd.

Abstract

Background: MicroRNAs (miRNAs) are small endogenous RNAs with an approximate length of 18-22 nucleotides and involved in the regulation of gene expression in transcriptional or post-transcriptional levels. They were found to be associated with leaf morphogenesis, flowering time, vegetative phase change, and response to environmental cues in plants, where they act as a critical regulatory factor. The nature of high conservancy of plant miRNAs within the plant species made it possible to detect the conserved miRNAs by computational approaches. Expressed Sequence Tags (EST) based comparative genomic approaches provide advantages over wet lab approaches as it is convenient, easy to carry out and less time consuming. EST-based in silico approach can unravel new conserved miRNAs in plants, even when the complete genome sequence is not available.

Results: To identify the novel miRNAs, a total of 46,865 ESTs from Jatropha curcas were searched for homology to all available 6746 mature miRNAs of plant eudicotyledons. Finally, we ended up with 12 novel miRNAs in Jatropha that range from 18 to 19 nucleotides where their respective precursor miRNAs had 54.11-71.76% (A + U) content. The putative miRNAs belong to 12 individual miRNA family and most of them have higher (A + U) content ranging from 47.36 to 77.77% than their respective miRNA homologs. Many of the target genes by the newly identified miRNAs were associated with plant growth and development, stress response, defense and hormone signaling, and oil synthesis pathways.

Conclusion: These findings have the potential to speed up miRNA identification and expand our understanding of miRNA functions in J. curcas.

Keywords: Bioinformatics; Conserved miRNAs; Jatropha curcas; Phylogenetic analysis.