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Identification, expression analysis, and potential roles of microRNAs in the regulation of polysaccharide biosynthesis in Polygonatum cyrtonema Hua

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Abstract

MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs with important roles in plant growth, development, and metabolic processes. Polygonatum cyrtonema Hua (P. cyrtonema) is an important Chinese traditional medicinal herb with broad pharmacological functions, and polysaccharides are the main biological substance accumulated in the P. cyrtonema rhizome. However, regulation of the process of polysaccharide biosynthesis in P. cyrtonema remains largely unknown.To elucidate the miRNAs and their targets involved in polysaccharide biosynthesis in P. cyrtonema, four small RNA libraries were constructed from flower, leaf, rhizome, and root tissues and sequenced. A total of 69 conserved and 5 novel miRNAs were identified, of which 6 miRNAs (miR156a-5p, miR156f-5p, miR395a-5, miR396a-3p, miR396g-3p, and miR397-5p-1) were down-regulated and 7 miRNAs (miR160, miR160h-1, miR160e-5p, miR319b-1, miR319-1, miR319c-5p-3, and miR319c-1) were up-regulated in rhizomes compared with flower, leaf, and root tissues. Bioinformatics analysis showed that the predicted targets of these miRNAs were mostly transcription factors and functional genes enriched in metabolic and secondary metabolite biosynthetic pathways, and 7 genes and their paired miRNAs were identified in carbohydrate metabolism. qRT-PCR expression analysis demonstrated that 6 miRNAs and their targets involved in carbohydrate metabolism were existed a negative correlation in. P. cyrtonema tissues. MiR396a-3p and one of its target genes, abfA, were possibly involved in polysaccharide biosynthesis pathway. This is the first report on the identification of conserved and novel miRNAs and their potential targets in P. cyrtonema, thus providing molecular evidence for the role of miRNAs in the regulation of polysaccharide biosynthesis in P. cyrtonema.

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Data availability

The sRNA-Seq data sets of four P. cyrtonema tissues have been deposited in NCBI Sequence Read Archive (SRA) database under the accession number SRP193031. The RNA-seq data sets of four P. cyrtonema tissues have been deposited in NCBI Sequence Read Archive (SRA) database under the accession number SRP193176.

Abbreviations

miRNA:

MicroRNA

qRT-PCR:

Quantitative real-time PCR

DEM:

Differentially expressed miRNA

GO:

Gene ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

sRNA:

Small RNA

TPM:

Transcripts per kilobase million

SPL:

Squamosa promoter-binding protein-like

ARF:

Auxin response factor

MYB:

V-myb avian myeloblastosis viral oncogene homolog

TCP:

Teosinte branched1/Cincinnata/proliferating cell factor

abfA:

Alpha-L-arabinofuranosidase

GalDH:

L-galactose dehydrogenase

SORD:

L-iditol 2-dehydrogenase

SDHA:

Succinate dehydrogenase

PSPs:

Polygonatum polysaccharides

GRF1:

Growth-regulating factor1

SAMT:

Salicylic acid carboxyl methyltransferase

GHs:

Glycosyl hydrolases

NBS-LRR:

Nucleotide-binding site-leucine-rich repeat

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Acknowledgements

We thank the Beijing Genomics Institute for assistance with experiments.

Funding

The financial support for the development and completion of this project was provided by startup funds through Natural Science Research Grant of Higher Education of Anhui Province (Grant Number KJ2019A0476, KJ2018ZD028) and Natural Science Foundation of Anhui Province of China (Grant Number 2008085MH268, 2108085MH315). The National Key Research and Development Program (Grant Number 2017YFC1701600) and the National project cultivation fund of Anhui University of Chinese Medicine (Grant Number 2020PY02) provided experimental support. Publication costs were funded by Outstanding Youth general Project of Anhui Institution of Higher Education (Grant Number gxyq2019030).

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Authors and Affiliations

  1. Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China

    Kelong Ma, Shengxiang Zhang, Liqiang Zhao, Chenkai Wang, Yuanyuan Shi, Qingshan Yang & Jiawen Wu

  2. College of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China

    Kelong Ma

  3. Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038, China

    Shengxiang Zhang, Liqiang Zhao, Chenkai Wang, Yuanyuan Shi & Jiawen Wu

  4. Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230012, China

    Qingshan Yang & Jiawen Wu

Authors
  1. Kelong Ma
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  2. Shengxiang Zhang
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  3. Liqiang Zhao
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Contributions

Project design: J.W.W. Experiments and data analysis: K.L.M., S.X.Z., Z.L.Q., C.K.W., and Y.Y.S. Manuscript preparation: K.L.M. Preparation of plant materials: Q.S.Y. All authors read and approved the final manuscript.

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Correspondence to Jiawen Wu.

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Ma, K., Zhang, S., Zhao, L. et al. Identification, expression analysis, and potential roles of microRNAs in the regulation of polysaccharide biosynthesis in Polygonatum cyrtonema Hua. J. Plant Biochem. Biotechnol. 31, 925–937 (2022). https://doi.org/10.1007/s13562-022-00772-7

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