Science China Life Sciences

, Volume 61, Issue 2, pp 178–189 | Cite as

An expression atlas of miRNAs in Arabidopsis thaliana

Research Paper


MicroRNAs (miRNAs) are small non-coding RNAs that regulate a variety of biological processes. MiRNA expression often exhibits spatial and temporal specificity. However, genome-wide miRNA expression patterns in different organs during development of Arabidopsis thaliana have not yet been systemically investigated. In this study, we sequenced small RNA libraries generated from 27 different organ/tissue types, which cover the entire life cycle of Arabidopsis. Analysis of the sequencing data revealed that most miRNAs are ubiquitously expressed, whereas a small set of miRNAs display highly specific expression patterns. In addition, different miRNA members within the same family have distinct spatial and temporal expression patterns. Moreover, we found that some miRNAs are produced from different arms of their hairpin precursors at different developmental stages. This work provides new insights into the regulation of miRNA biogenesis and a rich resource for future investigation of miRNA functions in Arabidopsis.


miRNA plant development high-throughput sequencing 


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This work was supported by grants fromNational Key Research and Development Program of China (2016YFA0500800) and National Natural Science Foundation of China (31421001, 31225015) to Yijun Qi. Yijun Qi is a visiting investigator of the CAS Center for Excellence in Molecular Plant Sciences.

Supplementary material

11427_2017_9199_MOESM1_ESM.pdf (921 kb)
Figure S1 Correlation between two biological replicates of small RNA sequencing.
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Figure S2 Small RNA size distribution and 5′ bias.
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Figure S3 S-plots for miRNAs.
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Figure S4 Expression pattern and strand bias of conserved versus non-conserved miRNAs.
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Figure S5 Expression of representative miRNAs at vegetative stages.
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Figure S6 Analysis of miRNA arm switch events.
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Table S1 Summary of small RNA libraries used in this study
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Table S2 Expression levels of miRNAs in all samples
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Table S3 Expression levels of members of highly conserved miRNA families during development
11427_2017_9199_MOESM10_ESM.pdf (114 kb)
Table S4 The sequences of probes used in small RNA Northern blot


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© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Center for Plant Biology, School of Life SciencesTsinghua UniversityBeijingChina
  2. 2.Tsinghua-Peking Center for Life SciencesBeijingChina
  3. 3.College of Biological SciencesChina Agricultural UniversityBeijingChina
  4. 4.College of Life Sciences-Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental ImprovementCapital Normal UniversityBeijingChina

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