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Comparative Analysis and Functional Identification of Rhizome miRNAs of Two Atractylodes lancea Ecotypes

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Abstract

Plant microRNAs (miRNAs) are short, non-coding RNA molecules. They mediate RNA silencing and regulate a series of target mRNAs involved in plant development, metabolism, and responses to different ecological environments. As one of important medicinal plants, Atractylodes lancea has a high medicinal significance and commercial value. Mao and Dabie are two ecotypes of A. lancea which mainly distributes in Mao Mountain and Dabie Mountain, respectively. To better understand the genomic information and germplasm resource characteristics, miRNA profiling analysis by high-throughput sequencing was performed to identify rhizome miRNAs of two A. lancea ecotypes. A transcriptomic database was established to identify miRNAs precursors and their target transcripts. By comparing small RNAs and the transcriptomic database, 270 known miRNAs of 46 miRNA families and 91 novel miRNAs were identified, plus hundreds of putative targets. Using Mireap software, 5 and 12 of 22 significant differentially expressed miRNAs were involved in ecotype formation and terpenoid metabolism, respectively, which was verified by qRT-PCR tests. These results are an important resource to better understand the biological mechanism of terpene formation and A. lancea adaptation to different ecological environment.

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Data availability

The data that support the findings of this study are available on request from the corresponding author upon reasonable request.

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Acknowledgements

The authors express their sincere thanks to the National Natural Science Foundation of China (Grant nos. 32000254 and 31670341) for their support.

Funding

National Natural Science Foundation of China, 32000254 and 31670341.

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Author notes

  1. Juan Deng, Lei Chen and Aisong Zhang have contributed equally to this work.

Authors and Affiliations

  1. College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People’s Republic of China

    Juan Deng, Lei Chen, Aisong Zhang, Meng Wang, Ling Gong, Wenjie Wang, Kun Yu & Bisheng Huang

  2. Hubei Key Laboratory of Resources and Chemistry of Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, People’s Republic of China

    Kun Yu

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  1. Juan Deng
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Contributions

KY and BH: designed the research. JD: and LC: performed the experiments, acquired and analyzed data, and drafted the manuscript. AZ: calculated the data and revised the manuscript. LG: and KY: have been involved in revising the manuscript critically for important intellectual content. MW and WW: contributed plants materials. All authors read and approved the final manuscript.

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Correspondence to Kun Yu or Bisheng Huang.

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Deng, J., Chen, L., Zhang, A. et al. Comparative Analysis and Functional Identification of Rhizome miRNAs of Two Atractylodes lancea Ecotypes. J. Plant Biol. 66, 135–145 (2023). https://doi.org/10.1007/s12374-023-09381-w

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