Identification of fenugreek (Trigonella foenum-graecum) microRNAs through deep sequencing and prediction of their potential regulatory roles in plant secondary metabolism

Plants have been indispensable for human civilization, for example, in medicine, where their secondary metabolites play a fundamental role. MicroRNAs (miRNAs), short non-coding riboregulators, are essential in the control of gene expression and offer potential therapeutic and bioengineering applications. Fenugreek (Trigonella foenum-graecum) has been a staple in Asian and African cuisines for centuries and has been shown to have significant medicinal and cosmetic benefits thanks to its high concentration of secondary metabolites; however, little is known about its miRNA profile. In this study, next-generation sequencing (NGS) technology was used to explore the miRNA landscape of T. foenum-graecum and its relationship with secondary metabolite biosynthesis. The analysis revealed 23,951,014 distinct reads, ranging from 16 to 40 nucleotides, identifying 287 conserved and 92 novel miRNAs. Furthermore, 10,313 potential target genes for fenugreek miRNAs were identified. Conserved and novel miRNAs were found targeting enzymes crucial for the biosynthesis pathways of terpenoids, diterpenoids, ubiquinones, carotenoids and flavonoids. These findings open the panorama for the use of transgenics mediated by miRNAs and the production of plant secondary metabolites, in addition to promoting industry applications at a commercial and medicinal level by improving the bioactivity and economic value of botanical resources such as fenugreek.