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High-throughput sequencing and degradome analysis reveal microRNA differential expression profiles and their targets in Paulownia fortunei

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Abstract

Paulownia fortunei (family Paulowniaceae) is an economically important tree species indigenous to China. Autotetraploid cultivars of P. fortunei have better growth and wood quality than their diploid counterparts. MicroRNAs (miRNAs) play vital regulatory roles in plant growth, development, and biotic and abiotic stress responses by direct cleavage of transcripts, translational repression, or chromatin modification. Although miRNAs have been identified in various plant species, no reports of miRNAs in P. fortunei have been published so far. To study the functions of miRNAs in the autotetraploid P. fortunei, four sequencing libraries from the autotetraploid and its corresponding diploid plants were constructed. 142 conserved miRNAs grouped into 41 families, and 38 novel miRNAs were obtained. Among these miRNAs, 58 were up-regulated and 30 were down-regulated in the autotetraploid relative to the diploid. MiRNA target genes were identified using a degradome sequencing approach and the differently expressed miRNAs and their target genes were validated by real time PCR analysis. To our knowledge, this is the first study to identify conserved and novel miRNAs and their potential targets from diploid and autotetraploid Paulownia plants using high-throughput sequencing and degradome analysis. Our results provide valuable information on P. fortunei miRNAs and their targets, and will help build a foundation for future studies of the biological functions of miRNA-mediated gene regulation in P. fortunei.

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Acknowledgments

This work was financially supported by the National Natural Science Foundation of China (Grant No. 30271082, 30571496, U1204309), by the Outstanding Talents Project of Henan Province (Grant No. 122101110700), by the Transformation Project of the National Agricultural Scientific and Technological Achievement of China (Grant No. 2012GB2D000271), 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, 95 Wenhua Road, Jinsui District, Zhengzhou, 450002, Henan, People’s Republic of China

    Suyan Niu, Guoqiang Fan, Zhenli Zhao, Minjie Deng & Yanpeng Dong

  2. College of Forestry, Henan Agricultural University, 95 Wenhua Road, Jinsui District, Zhengzhou, 450002, Henan, People’s Republic of China

    Suyan Niu, Guoqiang Fan, Zhenli Zhao, Minjie Deng & Yanpeng Dong

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  1. Suyan Niu
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  2. Guoqiang Fan
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  3. Zhenli Zhao
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  4. Minjie Deng
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  5. Yanpeng Dong
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Corresponding author

Correspondence to Guoqiang Fan.

Electronic supplementary material

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Supplementary material 1 (XLS 23 kb)

Supplementary material 2 (XLS 55 kb)

Supplementary material 3 (XLS 35 kb)

11240_2014_546_MOESM4_ESM.doc

Online Resource 4 The secondary structures of novel P. fortunei miRNA precursors. (The mature miRNAs are in red, and the miRNA*s are in green) (DOC 69 kb)

Supplementary material 5 (XLS 290 kb)

11240_2014_546_MOESM6_ESM.doc

Online Resource 6 Species distribution of the BLAST matches of the degradome targets. This figure shows the distributions of unigenes BLASTX matches against the nr protein database (cutoff value E < 10−5) and the proportions for each species (DOC 116 kb)

11240_2014_546_MOESM7_ESM.doc

Online Resource 7 GO analyses of the targets of the conserved and novel miRNAs in P. fortunei. Blue bar, indicate the Biological process; Red bar, indicate the Cellular component; Green bar, indicate the Molecular function (DOC 140 kb)

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Niu, S., Fan, G., Zhao, Z. et al. High-throughput sequencing and degradome analysis reveal microRNA differential expression profiles and their targets in Paulownia fortunei . Plant Cell Tiss Organ Cult 119, 457–468 (2014). https://doi.org/10.1007/s11240-014-0546-9

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