J Integr Plant Biol ›› 2015, Vol. 57 ›› Issue (3): 256-270.DOI: 10.1111/jipb.12239

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Identification of mRNA-like non-coding RNAs and validation of a mighty one named MAR in Panax ginseng

Meizhen Wang, Bin Wu, Chao Chen and Shanfa Lu*   

  • 收稿日期:2014-05-21 接受日期:2014-07-03 出版日期:2014-07-08 发布日期:2014-07-08

Identification of mRNA-like non-coding RNAs and validation of a mighty one named MAR in Panax ginseng

Meizhen Wang, Bin Wu, Chao Chen and Shanfa Lu*   

  1. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
  • Received:2014-05-21 Accepted:2014-07-03 Online:2014-07-08 Published:2014-07-08
  • About author:*Correspondence: E-mail: sflu@implad.ac.cn

摘要： MlncRNAs are a class of lncRNAs playing vital roles in plants. Through an integrative analysis of transcriptome, sRNAome and degradome, 3688 mlncRNAs were identified and characterized in Panax ginseng. One of them, termed MAR, was found to play significant regulatory roles in multiple metabolic pathways in a small RNA-dependent manner.

Abstract:

Increasing evidence suggests that long non-coding RNAs (lncRNAs) play significant roles in plants. However, little is known about lncRNAs in Panax ginseng C. A. Meyer, an economically significant medicinal plant species. A total of 3,688 mRNA-like non-coding RNAs (mlncRNAs), a class of lncRNAs, were identified in P. ginseng. Approximately 40% of the identified mlncRNAs were processed into small RNAs, implying their regulatory roles via small RNA-mediated mechanisms. Eleven miRNA-generating mlncRNAs also produced siRNAs, suggesting the coordinated production of miRNAs and siRNAs in P. ginseng. The mlncRNA-derived small RNAs might be 21-, 22-, or 24-nt phased and could be generated from both or only one strand of mlncRNAs, or from super long hairpin structures. A full-length mlncRNA, termed MAR (multiple-function-associated mlncRNA), was cloned. It generated the most abundant siRNAs. The MAR siRNAs were predominantly 24-nt and some of them were distributed in a phased pattern. A total of 228 targets were predicted for 71 MAR siRNAs. Degradome sequencing validated 68 predicted targets involved in diverse metabolic pathways, suggesting the significance of MAR in P. ginseng. Consistently, MAR was detected in all tissues analyzed and responded to methyl jasmonate (MeJA) treatment. It sheds light on the function of mlncRNAs in plants.

 

Wang M, Wu B, Chen C, Lu S (2015) Identification of mRNA‐like non‐coding RNAs and validation of a mighty one named MAR in Panax ginseng. J Integr Plant Biol 57: 256–270. doi: 10.1111/jipb.12239

Key words: MAR, miRNA, mlncRNA, Panax ginseng, siRNA

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