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A genome-wide identification and characterization of mircoRNAs and their targets in ‘Suli’ pear (Pyrus pyrifolia white pear group)

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Abstract

MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that are endogenous regulators of gene expression. miRNAs play a crucial role in cells via degradation of target mRNAs or by inhibition of target protein translation. In the present study, 186 new potentially conserved pear miRNAs belonging to 37 families were identified. The length of mature miRNAs ranged from 19 to 24 nt, and most of the miRNAs (154 out of 186) were 21 nt in length. The length of pre-miRNAs in pear was also found to vary from 62 to 282 nt with an average of 105 ± 43 nt. The potential miRNAs belonged to 29 clusters involving 20 different miRNA families. Using these potential miRNAs, we further scoured of the pear genome and found 326 potential target genes, which included transcription factors, stress responsive genes, and the genes involved in transmembrane transport and signal transduction. Gene ontology analysis of these potential targets suggested that 47 biological processes were potentially regulated by miRNAs, including oxidation–reduction, stress response, transport, etc. KEGG pathway analysis showed that the identified miRNAs were found in 15 metabolism networks which were related to starch and sucrose metabolism, and ascorbate and aldarate metabolism, among others. Our study will help in the further understanding of the essential role of miRNAs in growth and development and stress response of pear.

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Abbreviations

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

miRNAs:

MicroRNAs

MFE:

Minimal folding free energy

MFEI:

Minimal folding free energy index

nt:

Nucleotide

pre-miRNAs:

MiRNAs precursor

NCBI:

National center for biotechnology information

HTGS:

High through-put genomic sequences

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (No. 31272141) and the earmarked fund for Modern Agro-industry Technology Research Systems (nycytx-29-14).

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Authors and Affiliations

  1. Department of Horticulture, The State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, 310058, China

    Qingfeng Niu, Minjie Qian, Guoqin Liu, Fengxia Yang & Yuanwen Teng

  2. College of Agriculture, Guizhou University, Guiyang, 550025, China

    Guoqin Liu

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  1. Qingfeng Niu
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  2. Minjie Qian
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  3. Guoqin Liu
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  4. Fengxia Yang
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  5. Yuanwen Teng
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Corresponding author

Correspondence to Yuanwen Teng.

Additional information

Q. Niu and M. Qian contributed equally to this work.

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Niu, Q., Qian, M., Liu, G. et al. A genome-wide identification and characterization of mircoRNAs and their targets in ‘Suli’ pear (Pyrus pyrifolia white pear group). Planta 238, 1095–1112 (2013). https://doi.org/10.1007/s00425-013-1954-5

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  • DOI: https://doi.org/10.1007/s00425-013-1954-5

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