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<p><i>Ocimum sanctum </i> L. (Os) and <i>Ocimum basilicum </i> L. (Ob) exhibit significant commercial value as they produce important therapeutic secondary metabolites. miRNAs are small, non-coding RNAs, and their contribution to regulating Os and Ob secondary metabolism is largely unexplored. To unravel this, the leaf transcriptomes of Os and Ob were <i>de novo</i> assembled, yielding 85,659 and 103,356 unigenes, respectively. By employing the homology-based approach, 13 and 14 promising miRNAs were predicted in Os and Ob, respectively, from 8 families, with 6 miRNAs common between both species. Target prediction and functional annotation revealed 11 miRNAs in Ob regulate 21 targets, and 12 of the 13 in Os target 32 genes involved in secondary metabolism, with 12 being common to both plant miRNAs. To confirm the predicted results, 6 miRNAs and their target genes from both plants were subjected to qRT-PCR analysis. Relative expression analysis showed 56.20-fold increase for ocs-miR396a-3p in Os, while a 186.19-fold increase was identified for ocb-miR166-3p in Ob, which was found to target key secondary metabolite biosynthetic enzymes. The findings may advance our understanding of miRNA-mediated regulation in this species and support the use of artificial-miRNA strategy to enhance the production of economically important secondary metabolites <i>via</i> metabolic engineering.</p>

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Comparative Transcriptome Analysis of Ocimum sanctum L. and Ocimum basilicum L. Deciphering MicroRNAs-Mediated Regulation of Secondary Metabolite Biosynthesis

  • 期刊论文

  • 发表日期：

    2026年3月17日

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  • Aqib Sarfraz,
  • Kahkashan Khatoon,
  • Laiq Ur Rahman,
  • Feroz Khan

摘要

Ocimum sanctum L. (Os) and Ocimum basilicum L. (Ob) exhibit significant commercial value as they produce important therapeutic secondary metabolites. miRNAs are small, non-coding RNAs, and their contribution to regulating Os and Ob secondary metabolism is largely unexplored. To unravel this, the leaf transcriptomes of Os and Ob were de novo assembled, yielding 85,659 and 103,356 unigenes, respectively. By employing the homology-based approach, 13 and 14 promising miRNAs were predicted in Os and Ob, respectively, from 8 families, with 6 miRNAs common between both species. Target prediction and functional annotation revealed 11 miRNAs in Ob regulate 21 targets, and 12 of the 13 in Os target 32 genes involved in secondary metabolism, with 12 being common to both plant miRNAs. To confirm the predicted results, 6 miRNAs and their target genes from both plants were subjected to qRT-PCR analysis. Relative expression analysis showed 56.20-fold increase for ocs-miR396a-3p in Os, while a 186.19-fold increase was identified for ocb-miR166-3p in Ob, which was found to target key secondary metabolite biosynthetic enzymes. The findings may advance our understanding of miRNA-mediated regulation in this species and support the use of artificial-miRNA strategy to enhance the production of economically important secondary metabolites via metabolic engineering.