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Planta

, 251:49 | Cite as

Computational screening of miRNAs and their targets in leaves of Hypericum spp. by transcriptome-mining: a pilot study

  • Linda PetijováEmail author
  • Zuzana Jurčacková
  • Eva Čellárová
Original Article

Abstract

Main conclusion

Our work provides a survey of mature miRNAs, their target genes and primary precursors identified by in-silico approach in leaf transcriptomes of five selected Hypericum species.

Abstract

MiRNAs are small non-coding RNA molecules found in animals, terrestrial plants, several algae and molds. As their role lies in the post-transcriptional gene silencing, these tiny molecules regulate many biological processes. Phyto-miRNAs are considered the important regulators of secondary metabolism in medicinal plants. The genus Hypericum comprises many producers of bioactive compounds, mainly unique naphtodianthrones with a great therapeutic potential. The main goal of our work was to identify genetically conserved miRNAs, characterize their primary precursors and target sequences in the leaf transcriptomes of five Hypericum species using in-silico approach. We found 20 sequences of potential Hypericum pri-miRNAs, and predicted and computationally validated their secondary structures. The mature miRNAs were identified by target genes screening analysis. Whereas predicted miRNA profiles differed in less genetically conserved families, the highly conserved miRNAs were found in almost all studied species. Moreover, we detected several novel highly likely miRNA–mRNA interactions, such as mir1171 with predicted regulatory role in the biosynthesis of melatonin in plants. Our work contributes to the knowledge of Hypericum miRNAome and miRNA–mRNA interactions.

Keywords

Bioinformatic analysis Primary miRNAs Melatonin Secondary metabolism 

Notes

Acknowledgements

The work was supported by the Slovak Research and Development Agency under Grant number APVV-18-0125 and the Scientific Grant Agency of Slovak Republic under Grant number VEGA 1/0013/19.

Supplementary material

425_2020_3342_MOESM1_ESM.xlsx (58 kb)
Online resource S1 Putative miRNAs and their target genes identified in H. perforatum leaf transcriptome (XLSX 58 kb)
425_2020_3342_MOESM2_ESM.xlsx (69 kb)
Online resource S2 Putative miRNAs and their target genes identified in H. androsaemum leaf transcriptome (XLSX 69 kb)
425_2020_3342_MOESM3_ESM.xlsx (65 kb)
Online resource S3 Putative miRNAs and their target genes identified in H. kalmianum leaf transcriptome (XLSX 65 kb)
425_2020_3342_MOESM4_ESM.xlsx (56 kb)
Online resource S4 Putative miRNAs and their target genes identified in H. annulatum leaf transcriptome (XLSX 56 kb)
425_2020_3342_MOESM5_ESM.xlsx (59 kb)
Online resource S5 Putative miRNAs and their target genes identified in H. tomentosum leaf transcriptome (XLSX 59 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2020

Authors and Affiliations

  • Linda Petijová
    • 1
    Email author
  • Zuzana Jurčacková
    • 1
  • Eva Čellárová
    • 1
  1. 1.Department of Genetics, Faculty of Science, Institute of Biology and EcologyP. J. Šafárik University in KošiceKošiceSlovak Republic

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