Abstract
Myco-heterotroph Monotropa hypopitys is a widely spread perennial herb used to study symbiotic interactions and physiological mechanisms underlying the development of non-photosynthetic plant. Here, we performed, for the first time, transcriptome-wide characterization of M. hypopitys miRNA profile using high throughput Illumina sequencing. As a result of small RNA library sequencing and bioinformatic analysis, we identified 55 members belonging to 40 families of known miRNAs and 17 putative novel miRNAs unique for M. hypopitys. Computational screening revealed 206 potential mRNA targets for known miRNAs and 31 potential mRNA targets for novel miRNAs. The predicted target genes were described in Gene Ontology terms and were found to be involved in a broad range of metabolic and regulatory pathways. The identification of novel M. hypopitys-specific miRNAs, some with few target genes and low abundances, suggests their recent evolutionary origin and participation in highly specialized regulatory mechanisms fundamental for non-photosynthetic biology of M. hypopitys. This global analysis of miRNAs and their potential targets in M. hypopitys provides a framework for further investigation of miRNA role in the evolution and establishment of non-photosynthetic myco-heterotrophs.
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Acknowledgments
This work was supported by a Grant from the Russian Science Foundation (14-24-00175), and was done with the use of the experimental climate control facility.
Author’s contribution
Conceived and designed the experiments: N.V.R., E.B.P., K.G.S. Performed the experiments: A.M.M., E.Z.K. Analyzed the data: A.V.B., A.V.S., O.A.S. Contributed reagents, materials, and analysis tools: N.V.R, E.B.P, A.V.B. Provided plant material: E.Z.K. Wrote the paper: A.V.S. All authors read and approved the final manuscript.
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Electronic supplementary material
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ESM_1 Supplementary Table S1
Summary of high-throughput sequencing of M. hypopitys small RNA library (PDF 164 kb)
ESM_2 Supplementary Table S2
Known mhy-miRNAs and their targets in M. hypopitys (XLSX 49 kb)
ESM_3 Supplementary Table S3
M. hypopitys miRNA isoforms (PDF 273 kb)
ESM_4 Supplementary Table S4
Identified precursors of known and candidate novel mhy-miRNAs, and novel mhy-miRNA targets (XLSX 24 kb)
ESM_5 Supplementary Figure S1
Secondary pre-miRNA structures of known conserved (1A - 1D) and candidate novel (1E - 1U) mhy-miRNAs. 1A shows pre-mhy-miR116a; 1B - pre-mhy-miR167a; 1C - pre-mhy-miR393ab; 1D - pre-mhy-miR1094c; 1E - pre-mhy-miR0001; 1F - pre-mhy-miR0007; 1G - pre-mhy-miR0008; 1H - pre-mhy-miR0009; 1I - pre-mhy-miR0013; 1 J - pre-mhy-miR0017; 1 K - pre-mhy-miR0026; 1L - pre-mhy-miR0036; 1 M - pre-mhy-miR0037; 1 N - pre-mhy-miR0039; 1O - pre-mhy-miR0044; 1P - pre-mhy-miR0045; 1Q - pre-mhy-miR0046; 1R - pre-mhy-miR0048; 1S - pre-mhy-miR00053; 1T - pre-mhy-miR0054; 1U - pre-mhy-miR0060 (PDF 1165 kb)
ESM_6 Supplementary Table S5
Selected target genes of M. hypopitys miRNAs compared to known plant miRNAs (PDF 309 kb)
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Shchennikova, A.V., Beletsky, A.V., Shulga, O.A. et al. Deep-sequence profiling of miRNAs and their target prediction in Monotropa hypopitys . Plant Mol Biol 91, 441–458 (2016). https://doi.org/10.1007/s11103-016-0478-3
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DOI: https://doi.org/10.1007/s11103-016-0478-3