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Identification and analysis of RNA editing sites in chloroplast transcripts of kenaf (Hibiscus cannabinus L.)

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Abstract

RNA editing is one of the post-transcriptional modification processes and can lead to changes in sequencing and functioning of corresponding proteins and genetic information. To reveal the composition and characteristic of RNA editing of kenaf chloroplast genome, the RNA editing sites in kenaf chloroplast were predicted and identified using bioinformatics and RT-PCR analysis. The prediction results showed a total of 48 editing sites distributed in 22 genes, all of them were C to U conversion leading to amino acid changes. Further analysis of the position of RNA editing sites revealed that except 11 editing sites located at the first codon base, the other editing sites were found at the second codon base. Then four genes were randomly selected to validate the editing sites. Results showed that it was accurate to study the chloroplast RNA editing sites by bioinformatics method accompanied with cloning sequencing. Furthermore, the protein secondary structure and transmembrane domain of ndhD and atpA that had undergone gene editing also changed after editing. This implied that proteins with structural changes may have an impact on kenaf growth. Meanwhile, the differential editing site was found in chloroplast transcripts in kenaf CMS line and its maintainer line, indicating that chloroplast RNA editing could be associated with kenaf CMS. Therefore, the present study laid a foundation to further reveal the biological functioning of chloroplast RNA editing in CMS and its maintainer lines in kenaf.

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Acknowledgements

All the authors are thankful for Guangxi Post-doctoral Special Fund (Y201002061), China Postdoctoral Science Foundation funded project (2018M643379), Natural Science Foundation of Guangxi (2018JJB130096). We also thank professor Ruiyang Zhou for providing materials.

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  1. Danfeng Tang and Fan Wei contributed equally to this work.

Authors and Affiliations

  1. College of Agriculture, Guangxi University, Nanning, China

    Danfeng Tang, Fan Wei, Muhammad Haneef Kashif, Fazal Munsif & Ruiyang Zhou

  2. Guangxi Botanical Garden of Medicinal Plants, Nanning, China

    Danfeng Tang & Fan Wei

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  1. Danfeng Tang
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  2. Fan Wei
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  3. Muhammad Haneef Kashif
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  4. Fazal Munsif
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Contributions

WF, FM and MHK helped perform the experiments and write the manuscript; TDF conducted the experiments and edited the article. TDF and ZRY approved the version to be published.

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Correspondence to Danfeng Tang or Ruiyang Zhou.

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Tang, D., Wei, F., Kashif, M.H. et al. Identification and analysis of RNA editing sites in chloroplast transcripts of kenaf (Hibiscus cannabinus L.). 3 Biotech 9, 361 (2019). https://doi.org/10.1007/s13205-019-1893-3

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