Abstract
Superfruit guava (Psidium guajava L.) is one of the healthiest fruits due to its high antioxidant dietary fiber and vitamin content. However, the growth and development of this plant are severely affected by salinity stress, mostly at the seedling stage. MicroRNAs (miRNAs) are small, noncoding, endogenous, highly conserved RNA molecules that play key regulatory roles in plant development, organ morphogenesis, and stress response signaling. In this study, applying computational approaches and following high stringent filtering criteria, a total of 40 potential microRNAs belonging to 19 families were characterized from guava. The identified miRNA precursors formed stable stem-loop structures and exhibited high sequence conservation among diverse and evolutionarily distant plant species. Differential expression pattern of seven selected guava miRNAs (pgu-miR156f-5p, pgu-miR160c-5p, pgu-miR162-3p, pgu-miR164b-5p, pgu-miR166t, pgu-miR167a-5p, and pgu-miR390b-5p) were recorded under salinity stress and pgu-miR162-3p, pgu-miR164b-5p as well as pgu-miR166t were found to be the most affected ones. Using the psRNATarget tool, a total of 49 potential target transcripts of the characterized guava miRNAs were identified in this study which are mostly involved in metabolic pathways, cellular development, and stress response signaling. A biological network has also been constructed to understand the miRNA mediated gene regulation using the minimum free energy (MFE) values of the miRNA-target interaction. To the best of our knowledge, this is the first report of guava miRNAs and their targets.
Highlights
MicroRNAs are highly conserved, 20–24 nucleotides long non-coding RNA molecules that play critical roles in post-transcriptional gene regulation either by triggering transcriptional repression or via targeting mRNA degradation [1,2]
We performed an in silico analysis to predict and identify potential guava miRNAs using a reference set of plant miRNAs obtained from the miRbase database [24]
To address whether the salinity stress influences the expression of the selectedpgu-miR167a-5p, guava miRNAs (pgu-miR156f-5p, pgu-miR160c-5p, pgu-miR162-3p, pgu-miR164b-5p, pgu-miR166t, in leaves, a qRT-PCR experiment was carried out and the results showed and the pgu-miR390b-5p) in leaves, a qRT-PCR experiment was carried out and the results showed the differential expression of all the 7 miRNA under salinity stress
Summary
MicroRNAs (miRNAs) are highly conserved, 20–24 nucleotides (nt) long non-coding RNA molecules that play critical roles in post-transcriptional gene regulation either by triggering transcriptional repression or via targeting mRNA degradation [1,2]. MicroRNA biogenesis in plants begins when miRNA genes are transcribed into long primary transcripts (pri-miRNAs) by the enzyme RNA polymerase II. The resulting pri-miRNAs are cleaved to generate stem-loop RNA precursors (pre-miRNAs) by ribonuclease III-like Dicer (DCL1) enzyme. The only sequence-based in silico homology approaches to identify potential miRNAs in new plant species may yield false-positive results, and consideration must be given to the secondary structures as well as other parameters of the pre-miRNAs such as length, GC content, Minimum Folding Free
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