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Deep sequencing discovery of novel and conserved microRNAs in wild type and a white-flesh mutant strawberry

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Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by base pairing to mRNA target sequences, and play crucial roles in plant development and stress responses. The knowledge on post-transcriptional regulation by miRNAs in strawberry is rather limited so far. In order to understand the role of miRNA in the molecular control during strawberry fruit development, small RNA libraries were constructed from fruits at the turning stage of strawberry cultivar ‘Sachinoka’ and its white-flesh mutant by using the Solexa platform. One hundred and twenty conserved miRNAs belonging to 27 miRNA families and 33 putative novel strawberry miRNAs were identified in both libraries. Their target genes were predicted using the Fragaria vesca genome. Nine of all miRNAs showed significant expression differences between two types of samples. Four miRNAs were up-regulated and five were down-regulated in white-flesh mutant. The sequencing results were partially validated by quantitative RT-PCR. Among them, the expression of miR399a shows the biggest change between the two samples. The prediction of its target gene showed that miR399 may play an important role in phosphate homeostasis of strawberry fruits. Furthermore, we deduce that the expression of miR399 has negative correlation with the content of sugars.

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Abbreviations

dNTP:

Deoxynucleotide triphosphate

MFE:

Minimal folding free energy

miRNA:

MicroRNA

MT:

Mutant type

NCBI:

National Center for Biotechnology Information

pre-miRNA:

miRNA precursor

pri-miRNA:

Primary miRNA

qRT-PCR:

Quantitative reverse transcription-polymerase chain reaction

RISC:

RNA-induced silencing complex

WT:

Wild type

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Acknowledgments

This work was financially supported by National Natural Science Foundation of China (31101524), Special Fund for Agro-scientific Research in the Public Interest (201003064), Postdoctoral Foundation of China (20100481212 and 2012T50270) and Program for Innovation Team in University of Liaoning Province (LT2010094).

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Correspondence to Zhihong Zhang.

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Li, H., Mao, W., Liu, W. et al. Deep sequencing discovery of novel and conserved microRNAs in wild type and a white-flesh mutant strawberry. Planta 238, 695–713 (2013). https://doi.org/10.1007/s00425-013-1917-x

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Keywords

  • Fruit development
  • Fragaria × ananassa
  • MicroRNA
  • Solexa sequencing
  • qRT-PCR