Research article
Identification of miRNAs and their targets involved in the secondary metabolic pathways of Mentha spp.

https://doi.org/10.1016/j.compbiolchem.2016.06.004Get rights and content

Highlights

  • Eleven miRNAs families and 130 target transcripts were identified.

  • Predicted miRNAs were involved in different metabolic process.

  • miR156, miR414 and miR5021 showed regulation of essential oil biosynthesis.

  • Three miRNAs were involved in trichome development.

Abstract

The endogenous, small and non-coding functional microRNAs govern the regulatory system of gene expression and control the growth and development of the plants. Mentha spp. are well known herbs for its flavor, fragrance and medicinal properties. In the present study, we used a computational approach to identify miRNAs and their targets involved in different secondary metabolic pathways of Mentha spp. Additionally, phylogenetic and conservation analysis were also done for the predicted miRNAs. Eleven miRNAs families were identified from Mentha spp., out of which five miRNA families were reported for the first time from Lamiaceae. Overall, 130 distinct target transcripts were predicted for eight miRNAs families. All the predicted targets regulated by predicted miRNAs control the reproduction, signaling, stimulus response, developmental and different metabolic process. miRNA mediated gene regulatory network was also constructed on the basis of hybridized minimum free energy of identified miRNAs and their targets. The study revealed that the gene regulatory system of essential oil biosynthesis may be governed by miR156, miR414 and miR5021 in mint family. Furthermore, three miRNA candidates (miR156, miR5021, and miR5015b) were observed to be involved in trichome development also. This is the first in-silico study describing miRNAs and their role in the regulation of secondary metabolic pathways in Mentha spp.

Graphical abstract

The study revealed that essential oil biosynthesis in Mentha spp. may be governed by miR156, miR414 and miR5021. Three miRNA candidates (miR156, miR5021, and miR5015b) were observed to be involved in trichome development. This is the first in-silico study describing miRNAs and their role in the regulation of secondary metabolic pathways in Mentha spp.

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Introduction

microRNAs are one of the small, non-coding, regulatory molecule, which regulate gene expression in many organisms by transcriptional cleavage or translational suppression (Carrington and Ambros, 2003, Bartel, 2004). Mints (Mentha spp.) are commercially important herbs used widely for their flavor, fragrance and medicinal properties (Karousou et al., 2007, Bassole et al., 2010, Chen et al., 2011, Mishellany-Dutour et al., 2012). Several reports are available on essential oil biosynthesis and its regulation in Mentha spp. (Champagne and Boutry, 2013, Colby et al., 1993; Dolzhenko et al., 2010). However, no work has been reported on the role of miRNAs in the regulation of essential oil biosynthesis and other secondary metabolite pathways of Mentha spp.

The computational screening of potential miRNAs is cost-effective, fast and favorable method. Lower expression of the gene in the experimental techniques makes computational approach a preferable option. Several miRNAs were reported earlier by this approach (Jones-Rhoades and Bartel, 2004, Zhang et al., 2006b). Genome sequence, NGS data and Expressed Sequence Tags (ESTs) are the preferable elements for in-silico miRNA identification (Zhang et al., 2006a, Wu et al., 2011, Yu et al., 2011). Very few numbers of ESTs has been reported in the public domain for Mentha. Mentha spicata and Mentha aquatica were reported only for 178 and 73 numbers of ESTs, respectively. Mentha x piperita has a maximum number of 1316 ESTs reported. The lack of genome sequence and limited numbers of reported ESTs in public database works as a restrictive aspect for this investigation. To overcome this problem a combined transcriptome reads from several closely related species: Mentha x piperita, M. aquatica and M. spicata was used for the miRNAs and their target identification. In the present study, we identified miRNAs and their targets in Mentha spp. and analyzed their role in the regulation of secondary metabolite pathways, especially in essential oil biosynthesis.

Section snippets

Processing of assembly, microRNAs and their target identification

A combined transcriptome peppermint_parents_assembly_2012 was downloaded from the Mint Genomics Resource (http://langelabtools.wsu.edu/mgr/downloads). Assembly was derived from a pool of transcriptome reads from closely related species: Mentha x piperita, M. aquatica, and M. spicata. Experimental condition as mentioned in the Mint Genome Resource was as follows: glandular trichomes of Mentha spp. used for the mRNA isolation at two leaf developmental stages as young (less than half full length)

Identification of microRNAs and their characterization

A total of twenty four miRNAs families (Fig. 1), predicted by C-mii were filtered using different criteria. Some miRNA families as miR156, 160 and 164 were observed to have many members, predicted from the same transcript. To reduce false positive results and improve the accuracy, only single miRNA candidates predicted from single transcript with high MFEI(≦−0.6) were considered (Table 1). Filtered results were again evaluated by miRNA-dis. miR5658 was analyzed as false pre-miRNA by miRNA-dis.

Conclusions

Mint essential oil is widely used for its flavor, fragrance and medicinal properties. It is formed mainly by monoterpenes, which are products of the secondary metabolism. Eleven miRNA families were identified in three Mentha spp. (Mentha x piperita, M. aquatica, and M. spicata) by using a transcriptome assembly. Five miRNAs families were reported for the first time for Lamiaceae. Eight miRNA families were reported to have a total of 130 targets playing important role in growth and development.

Conflict of interest

The author declares that there is no conflict of interests regarding the publication of this article.

Acknowledgements

The financial support of the Department of Science and Technology (DST), New Delhi in the form of DST-INSPIRE-JRF (INSPIRE Fellow Code: IF120740) to the author Ms. Noopur Singh is gratefully acknowledged. The authors are also thankful for financial assistance under CSIR twelfth five year plan project BSC0203 (ChemBio).

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