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Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza

Abstract

Main conclusion

Identification and characterization of 5,446 mlncRNAs from Salvia miltiorrhiza showed that the majority of identified mlncRNAs were stress responsive, providing a framework for elucidating mlncRNA functions in S. miltiorrhiza.

mRNA-like noncoding RNAs (mlncRNAs) are transcribed by RNA polymerase II and are polyadenylated, capped and spliced. They play important roles in plant development and defense responses. However, there is no information available for mlncRNAs in Salvia miltiorrhiza Bunge, the first Chinese medicinal material entering the international market. To perform a transcriptome-wide identification of S. miltiorrhiza mlncRNAs, we assembled over 8 million RNA-seq reads from GenBank database and 5,624 ESTs from PlantGDB into 44422 unigenes. Using a computational identification pipeline, we identified 5446 S. miltiorrhiza mlncRNA candidates from the assembled unigenes. Of the 5446 mlncRNAs, 2 are primary transcripts of conserved miRNAs, and 2030 can be grouped into 470 families with at least two members in a family. Quantitative real-time PCR analysis of mlncRNAs with at least 900 nt showed that the majority were differentially expressed in roots, stems, leaves and flowers and responsive to methyl jasmonate (MeJA) treatment in S. miltiorrhiza. Analysis of published RNA-seq data showed that a total of 3,044 mlncRNAs were expressed in hairy roots of S. miltiorrhiza and the expression of 1,904 of the 3,044 mlncRNAs was altered by yeast extract and Ag+ treatment. The results indicate that the majority of mlncRNAs are involved in plant response to stress. This study provides a framework for understanding the roles of mlncRNAs in S. miltiorrhiza.

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Abbreviations

ncRNA:

Noncoding RNA

qRT-PCR:

Quantitative reverse-transcription PCR

sRNA:

Small RNA

miRNA:

MicroRNA

siRNA:

Small-interfering RNA

lncRNA:

Long noncoding RNA

mlncRNA:

mRNA-like noncoding RNA

pri-miRNA:

Primary miRNA

pre-miRNA:

miRNA precursor

DCL1:

Dicer-like 1

MeJA:

Methyl jasmonate

ORF:

Open reading frame

FDA:

Food and Drug Administration

HDS:

4-Hydroxy-3-methylbut-2-en-1-yl diphosphate synthase

SPS:

Solanesyl diphosphate synthase

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Acknowledgments

We thank Drs. Yingjie Zhu, Caili Li, Meizhen Wang and Suzhen Chen for kindly providing technical assistance. We appreciate Prof. Xian’en Li at the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College for providing S. miltiorrhiza plants. This work was supported by grants from the Natural Science Foundation of China (Grant No. 31370327), the Beijing Natural Science Foundation (Grant Nos. 5112026 and 5152021), the Major Scientific and Technological Special Project for Significant New Drugs Creation (Grant No. 2012ZX09301002-001-031), the Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20111106110033), and the Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT, Grant No. IRT1150).

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Correspondence to Shanfa Lu.

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Li, D., Shao, F. & Lu, S. Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza . Planta 241, 1131–1143 (2015). https://doi.org/10.1007/s00425-015-2246-z

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Keywords

  • Methyl jasmonate
  • mRNA-like noncoding RNA
  • Salvia
  • Traditional Chinese medicine
  • Transcriptome-wide analysis