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Dynamic landscape of mitochondrial Cytidine-to-Uridine RNA editing in tobacco (Nicotiana tabacum) shows its tissue specificity

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Abstract

RNA editing is a prevalent nucleotide modification at the RNA level in higher plants. However, little is known about the dynamic distribution of RNA editing among tissues. In this study, we explored the tissue specificity of mitochondrial RNA editing in tobacco (Nicotiana tabacum) based on publicly available RNA-seq data from four tobacco tissues: root, stem, leaf, and flower. As a result, 473 RNA editing sites involved in 60 mitochondrial genes were identified. The results showed an uneven distribution of editing sites among tobacco tissues, a total of 106 sites and 11 genes were identified as tissue-specific editing in the four tissues, and a total of 11 sites located in six genes were detected differentially edited statistically (p-value < 0.01). The expression of RNA edited genes and RNA editing factors was analyzed, and we observed that most tissue-specific edited genes were expressed at a low level. There were about ~  20 RNA editing factors that were differentially expressed between different tissues, indicating that the heterogeneity of RNA editing in different tissues might result from the expression regulation of RNA editing factors. Our analyses provide insights into the understanding of landscape, regulation, and function of RNA editing events in higher plants.

Key message

Dynamic landscape of conserved editing sites revealed the tissue specificity of mitochondrial RNA editing in tobacco.

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Abbreviations

C-to-U:

Cytidines substituting uridines

PPR:

Pentatricopeptide repeat

RNA-seq:

RNA sequencing

SNPs:

Single nucleotide polymorphisms

WGS:

Whole genome re-sequencing

cox1 :

Cytochrome coxidase subunit 1

ORFs:

Open reading frames

nad :

NADH dehydrogenase

MORF:

Multiple organelle RNA editing factors

rps :

Ribosomal protein gene

rps14 :

Ribosomal protein S14

ccmB :

Cytochrome c maturation gene

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Acknowledgements

We would like to thank the members of Bioinformatics Group of Wuhan Botanical Garden, Chinese Academy of Sciences, China for the discussion and suggestion to improve the manuscript.

Funding

This research was funded by the National Natural Science Foundation of China, Grant numbers 32070682 and 31702322, the National Science and Technology Innovation Zone Project, Grant numbers 1716315XJ00200303 and 1816315XJ00100216, and CAS Pioneer Hundred Talents Program.

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Authors and Affiliations

  1. Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China

    Jing Fang, Xiaohan Jiang, Tengfei Wang, Zhiyu Deng, Aidi Zhang & Xiujun Zhang

  2. Center of Economic Botany, Core Botanical Gardens, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China

    Jing Fang, Xiaohan Jiang, Tengfei Wang, Zhiyu Deng, Aidi Zhang & Xiujun Zhang

  3. University of Chinese Academy of Sciences, Beijing, China

    Jing Fang, Xiaohan Jiang, Tengfei Wang & Zhiyu Deng

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  1. Jing Fang
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  2. Xiaohan Jiang
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  3. Tengfei Wang
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  4. Zhiyu Deng
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  5. Aidi Zhang
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  6. Xiujun Zhang
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Contributions

Conceptualization, J.F., A.Z. and X.Z.; methodology, A.Z. and J.F.; software, A.Z and J.F.; validation, J.F. and A.Z.; formal analysis, J.F. and A.Z.; investigation, J.F. and A.Z.; resources, J.F. and A.Z.; data curation, J.F., T.W., Z.D. and A.Z.; writing original draft preparation, J.F. and A.Z.; writing, review and editing, A.Z. and X.Z.; visualization, J.F., X.J, and T.W.; supervision, X.Z.; project administration, X.Z.; funding acquisition, X.Z. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Aidi Zhang or Xiujun Zhang.

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Fang, J., Jiang, X., Wang, T. et al. Dynamic landscape of mitochondrial Cytidine-to-Uridine RNA editing in tobacco (Nicotiana tabacum) shows its tissue specificity. Plant Cell Tiss Organ Cult 148, 363–376 (2022). https://doi.org/10.1007/s11240-021-02194-0

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