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Discovery and profiling of microRNAs and their targets in Paulownia ‘Yuza 1’ plants via high-throughput sequencing and degradome analysis

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Abstract

Polyploid breeding is an effective method that has been used widely for the development of new varieties of plants. MicroRNAs (miRNAs) are a class of endogenous small RNAs that regulate gene expression at the post-transcriptional level. To understand the functions of miRNAs in autotetraploid and diploid Paulownia ‘Yuza 1’ plants, two small RNA libraries and two degradome sequencing libraries of the autotetraploid and the corresponding diploid plants were constructed and analyzed. A total of 49 conserved miRNAs that were grouped into 15 families, and 25 novel miRNAs were obtained from two sRNA libraries. Among these miRNAs, 28 were differentially expressed at a significant level in the autotetraploid relative to the diploid. Moreover, the miRNA target genes were identified by degradome sequencing and some of the differently expressed miRNAs and their target genes were validated by quantitative RT-PCR analysis. This study has provided valuable information on P. ‘Yuza 1’ miRNAs and their targets, which will enrich the Paulownia miRNA information resources and will contribute to our understanding of miRNA-mediated regulation in autotetraploid Paulownia plantlets.

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Acknowledgments

This work was financially supported by the National Natural Science Foundation of China (Grant Nos. 30271082, 30571496, U1204309), by the Outstanding Talents Project of Henan Province (Grant No.122101110700) and by Science and Technology Innovation Team Project of Zhengzhou City (Grant No. 121PCXTD515).

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Authors and Affiliations

  1. Institute of Paulownia, Henan Agricultural University, No 95 Wenhua Road, Zhengzhou, 450002, Henan, People’s Republic of China

    Xiaoqiao Zhai, Suyan Niu & Guoqiang Fan

  2. Forestry Academy of Henan, Zhengzhou, 450008, Henan, People’s Republic of China

    Xiaoqiao Zhai & Yuanyuan Ren

Authors
  1. Xiaoqiao Zhai
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  2. Suyan Niu
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  3. Yuanyuan Ren
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  4. Guoqiang Fan
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Correspondence to Guoqiang Fan.

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The authors declare that they have no conflict of interest.

Electronic supplementary material

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13258_2016_420_MOESM1_ESM.doc

Supplementary material 1 (DOC 150 kb) Fig S1 Hairpin structures of Paulownia ‘Yuza 1’ miRNAs. (miRNAs marked by yellow, miRNAs* marked by green)

Supplementary material 2 (DOC 39 kb) Table S1 The primers used for qRT-PCR

13258_2016_420_MOESM3_ESM.xls

Supplementary material 3 (XLS 32 kb) Table S2 Conserved miRNAs of Paulownia ‘Yuza 1’. (ath/aly Arabidopsis;ptc Populus trichocarp;osa Oryza sativa;zma Zea mays;gma Glycine max; + 2 mismatches; ++ 1 mismatches; +++ 0 mismatch)

13258_2016_420_MOESM4_ESM.xls

Supplementary material 4 (XLS 33 kb) Table S3 Novel miRNAs of Paulownia ‘Yuza 1’. (L Lenth;Ath Arabidopsis thaliana;Osa Oryza sativa;Egr Eucalyptus; × not matched to genomes; †matched to genomes)

Supplementary material 5 (XLS 29 kb) Table S4 Target gene identification and annotation

Supplementary material 6 (DOC 30 kb) Table S5 The comparison of conserved miRNAs numbers among four Paulownia species

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Zhai, X., Niu, S., Ren, Y. et al. Discovery and profiling of microRNAs and their targets in Paulownia ‘Yuza 1’ plants via high-throughput sequencing and degradome analysis. Genes Genom 38, 757–766 (2016). https://doi.org/10.1007/s13258-016-0420-8

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  • DOI: https://doi.org/10.1007/s13258-016-0420-8

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