Skip to main content
SpringerLink
Log in

A Bibliometric Study for Plant RNA Editing Research: Trends and Future Challenges

  • Review Paper
  • Published:
Molecular Biotechnology Aims and scope Submit manuscript

Abstract

RNA editing is a post-transcriptional process that introduces changes in RNA sequences encoded by nuclear, mitochondrial, or plastid genomes. To understand the research progress of plant RNA editing, we comprehensively analyze the articles on plant RNA editing from 2001 to 2022 through bibliometric methods. Nucleic Acids Research, Plant Journal and Plant cell are the journals that deserve attention with their high production, total local citation scores (TLCS), and h-indexes. The USA, China, and Germany are the top three countries with highly productive publications. Ulm University, Cornell University, and Chinese Acad Sci are excellent cooperative institutions with a high level of influence in the field, and KNOOP V and TAKENAKA M are good partnership. Plant RNA editing researches concentrate on the subject categories of Biochemistry & Molecular Biology, Plant Sciences, Genetics & Heredity, etc. Plant mitochondria, genome editing and messenger-RNA may be the research hotspots in the future. The main plant RNA editing research tools are JACUSA, SPRINT, and REDO, and the main databases are REDIdb, PED, and dbRES. At present, the research streams are (1) RNA editing sites; (2) Pentapeptide repeat protein (PPR) involved in RNA editing; (3) RNA editing factors. Overall, this article summarizes the research overview of plant RNA editing until 2022 and provides theoretical implications for its possible future directions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Source: authors’ compilation based on top 15 journals sorted by yearly total local citations (TLC/t). B The annual output of the journal. The horizontal axis represents the journal, the vertical axis is proportional to the time, and the different colors represent the number of journals

Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Data Availability

The data that support the findings of this study are available from the supplementary information.

References

  1. Benne, R., Van den Burg, J., Brakenhoff, J. P., Sloof, P., Van Boom, J. H., & Tromp, M. C. (1986). Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell, 46, 819–826.

    CAS  PubMed  Google Scholar 

  2. Covello, P. S., & Gray, M. W. (1989). RNA editing in plant-mitochondria. Nature, 341, 662–666.

    CAS  PubMed  Google Scholar 

  3. Hiesel, R., Wissinger, B., Schuster, W., & Brennicke, A. (1989). RNA editing in plant-mitochondria. Science, 246, 1632–1634.

    CAS  PubMed  Google Scholar 

  4. Gualberto, J. M., Lamattina, L., Bonnard, G., Weil, J. H., & Grienenberger, J. M. (1989). RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature, 341, 660–662.

    CAS  PubMed  Google Scholar 

  5. Edera, A. A., Gandini, C. L., & Sanchez-Puerta, M. V. (2018). Owards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria. Plant Molecular Biology, 97, 215–231.

    CAS  PubMed  Google Scholar 

  6. Lo Giudice, C., Hernández, I., Ceci, L. R., Pesole, G., & Picardi, E. (2019). RNA editing in plants: A comprehensive survey of bioinformatics tools and databases. Plant Physiology and Biochemistry, 137, 53–61.

    CAS  PubMed  Google Scholar 

  7. Cahoon, A., Nauss, J., Stanley, C., & Qureshi, A. (2017). Deep Transcriptome Sequencing of Two Green Algae, Chara vulgaris and Chlamydomonas reinhardtii. Provides No Evidence of Organellar RNA Editing Genes.

    Google Scholar 

  8. Ichinose, M., & Sugita, M. (2017). RNA editing and its molecular mechanism in plant organelles. Genes, 8, 5.

    Google Scholar 

  9. Gray, M. W. (2010). RNA editing in plant mitochondria: 20 years later. Iubmb Life.

    Google Scholar 

  10. Ichinose, M., & Sugita, M. (2017). RNA editing and its molecular mechanism in plant organelles. Genes. https://doi.org/10.3390/genes8010005

    Article  Google Scholar 

  11. Shikanai, T. (2015). RNA editing in plants: Machinery and flexibility of site recognition. Biochimica Biophysica Acta, 1847, 779–785.

    CAS  Google Scholar 

  12. Sun, T., Bentolila, S., & Hanson, M. R. (2016). The unexpected diversity of plant organelle RNA editosomes. Trends in Plant Science, 21, 962–973.

    CAS  PubMed  Google Scholar 

  13. Schallenberg-Rüdinger, M., & Knoop, V. (2016). Coevolution of organelle RNA EDITING and nuclear specificity factors in early land plants. Advances in Botanical Research, 78, 37–93.

    Google Scholar 

  14. Shen, L., Liang, Z., Wong, C. E., & Yu, H. (2019). Messenger RNA modifications in plants. Trends in Plant Science. https://doi.org/10.1016/j.tplants.2019.01.005

    Article  PubMed  Google Scholar 

  15. Ibtissam, J., Reddy, A., Maria, K., Saurabh, C., Waqas, K., Byrne, L. J., Wilson, C. M., & Syed, N. H. (2019). SURVEY AND SUMMARY Does co-transcriptional regulation of alternative splicing mediate plant stress responses?. Nuclc Acids Research, 47(6), 2716–2726.

    Google Scholar 

  16. Li, S., Wang, Y., Zhao, Y., Zhao, X., Chen, X., & Gong, Z. (2020). Global Co-transcriptional splicing in arabidopsis and the correlation with splicing regulation in mature RNAs. Molecular plant (English), 13(12), 266–277.

    CAS  Google Scholar 

  17. Mao, G. Z., Huang, N., Chen, L., & Wang, H. M. (2018). Research on biomass energy and environment from the past to the future: A bibliometric analysis. Science of the Total Environment, 635, 1081–1090.

    CAS  PubMed  Google Scholar 

  18. Chen, C., Hu, Z., Liu, S., & Tseng, H. (2012). Emerging trends in regenerative medicine: A scientometric analysis in CiteSpace. Expert Opinion on Biological Therapy, 12, 593–608.

    PubMed  Google Scholar 

  19. Van Eck, N. J., & Waltman, L. (2010). Software survey: VOSviewer, a computer program for bibliometric mapping. Scientometrics, 84, 523–538.

    PubMed  Google Scholar 

  20. Liu, H., Hong, R., Xiang, C., Lv, C., & Li, H. (2020). Visualization and analysis of mapping knowledge domains for spontaneous combustion studies. Fuel. https://doi.org/10.1016/j.fuel.2019.116598

    Article  PubMed  Google Scholar 

  21. Maditati, D. R., Munim, Z. H., Schramm, H.-J., & Kummer, S. (2018). A review of green supply chain management: From bibliometric analysis to a conceptual framework and future research directions. Resources Conservation And Recycling, 139, 150–162.

    Google Scholar 

  22. Kleinberg, J. (2003). Bursty and hierarchical structure in streams. Data Mining And Knowledge Discovery, 7, 373–397.

    Google Scholar 

  23. Hirsch, J. E. (2005). An index to quantify an individual’s scientific research output. Proceedings Of the National Academy Of Sciences Of the United States Of America, 102, 16569–16572.

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Chen, C. (2020). A Glimpse of the First Eight Months of the COVID-19 literature on microsoft academic graph: themes, citation contexts, and uncertainties. Frontiers in Research Metrics and Analytics, 5, 607286.

    PubMed  PubMed Central  Google Scholar 

  25. Chaomei, C., & Min, S. (2020). Visualizing a field of research: A methodology of systematic scientometric reviews. PLoS ONE, 14, e0223994.

    Google Scholar 

  26. Xu, W., Choi, H.-K., & Huang, L. (2017). State of Panax ginseng research: A global analysis. Molecules. https://doi.org/10.3390/molecules22091518

    Article  PubMed  PubMed Central  Google Scholar 

  27. Aria, M., & Cuccurullo, C. (2018). bibliometrix: An R-Tool for comprehensive science mapping analysis. Journal of Informetrics, 11, 959–975.

    Google Scholar 

  28. Aria, M., & Cuccurullo, C. (2017). bibliometrix: An R-Tool for comprehensive science mapping analysis. Journal Of Informetrics, 11, 959–975.

    Google Scholar 

  29. Du, P., Jia, L., & Li, Y. (2009). CURE-chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants. BMC Bioinformatics, 10, 135–135.

    PubMed  PubMed Central  Google Scholar 

  30. Du, P., Tao, H., & Li, Y. (2007). Prediction of C-to-U RNA editing sites in higher plant mitochondria using only nucleotide sequence features. Biochemical and Biophysical Research Communications, 358, 336–341.

    CAS  PubMed  Google Scholar 

  31. Howells, R. M., Craze, M., Bowden, S., & Wallington, E. J. (2018). Efficient generation of stable, heritable gene edits in wheat using CRISPR/Cas9. BMC Plant Biology. https://doi.org/10.1186/s12870-018-1433-z

    Article  PubMed  PubMed Central  Google Scholar 

  32. Malzahn, A. A., Tang, X., Lee, K., Ren, Q., & Qi, Y. (2019). Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis. BMC Biology, 17, 1–9.

    Google Scholar 

  33. Garfield, E., Paris, S. W., & Stock, W. C. (2006). HistCiteTrade: A software tool for informetric analysis of citation linkage. NFD Information—Wissenschaft und Praxis, 57, 391–400.

    Google Scholar 

  34. Tillich, M., Funk, H. T., Schmitz-Linneweber, C., Poltnigg, P., Sabater, B., Martin, M., & Maier, R. M. (2005). Editing of plastid RNA in Arabidopsis thaliana ecotypes. The Plant Journal, 43, 708–715.

    CAS  PubMed  Google Scholar 

  35. Tsudzuki, T., Wakasugi, T., & Sugiura, M. (2001). Comparative analysis of RNA editing sites in higher plant chloroplasts. Journal of Molecular Evolution, 53, 327–332.

    CAS  PubMed  Google Scholar 

  36. Freyer, R., KieferMeyer, M. C., & Kossel, H. (1997). Occurrence of plastid RNA editing in all major lineages of land plants. Proceedings Of the National Academy Of Sciences Of the United States Of America, 94, 6285–6290.

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Delannoy, E., Stanley, W. A., Bond, C. S., & Small, I. D. (2007). Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles. Biochemical Society Transactions, 35, 1643–1647.

    CAS  PubMed  Google Scholar 

  38. Okuda, K., Nakamura, T., Sugita, M., Shimizu, T., & Shikanai, T. (2006). A pentatricopeptide repeat protein is a site recognition factor in chloroplast RNA editing. Journal Of Biological Chemistry, 281, 37661–37667.

    CAS  PubMed  Google Scholar 

  39. Okuda, K., Chateigner-Boutin, A. L., Nakamura, T., Delannoy, E., Sugita, M., Myouga, F., Motohashi, R., Shinozaki, K., Small, I., & Shikanaia, T. (2009). Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in arabidopsis chloroplasts. The Plant Cell, 21, 146–156.

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Salone, V., Rudinger, M., Polsakiewicz, M., Hoffmann, B., Groth-Malonek, M., Szurek, B., Small, I., Knoop, V., & Lurin, C. (2007). A hypothesis on the identification of the editing enzyme in plant organelles. Febs Letters, 581, 4132–4138.

    CAS  PubMed  Google Scholar 

  41. Okuda, K., Myouga, F., Motohashi, R., Shinozaki, K., & Shikanai, T. (2007). Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing. Proceedings Of the National Academy Of Sciences Of the United States Of America, 104, 8178–8183.

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Bentolila, S., Heller, W. P., Sun, T., Babina, A. M., Friso, G., van Wijk, K. J., & Hanson, M. R. (2012). RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Proceedings Of the National Academy Of Sciences Of the United States Of America, 109, E1453–E1461.

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Hirose, T., & Sugiura, M. (2001). Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: Development of a chloroplast in vitro RNA editing system. Embo Journal, 20, 1144–1152.

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Du, P., Jia, L., & Li, Y. (2009). CURE-chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants. BMC Bioinformatics. https://doi.org/10.1186/1471-2105-10-135

    Article  PubMed  PubMed Central  Google Scholar 

  45. Lenz, H., Ruedinger, M., Volkmar, U., Fischer, S., Herres, S., Grewe, F., & Knoop, V. (2010). Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature. Current Genetics, 56, 189–201.

    CAS  PubMed  Google Scholar 

  46. Grewe, F., Viehoever, P., Weisshaar, B., & Knoop, V. (2009). A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii. Nucleic Acids Research, 37, 5093–5104.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Rüdinger, M., Funk, H. T., Rensing, S. A., & Knoop, M. V. (2009). RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal. Molecular Genetics & Genomics. https://doi.org/10.1007/s00438-009-0424-z

    Article  Google Scholar 

  48. Chaw, S. M., Chun-Chieh Shih, A., Wang, D., et al .(2008). The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites. Molecular Biology and Evolution, 25(3), 603–615.

    CAS  PubMed  Google Scholar 

  49. Picardi, E., & Pesole, G. (2013). REDItools: High-throughput RNA editing detection made easy. Bioinformatics, 29, 1813–1814.

    CAS  PubMed  Google Scholar 

  50. John, D., Weirick, T., Dimmeler, S., & Uchida, S. (2017). RNA Editor: Easy detection of RNA editing events and the introduction of editing islands. Briefings in Bioinformatics, 18, 993–1001.

    CAS  PubMed  Google Scholar 

  51. Wang, Z., Lian, J., Li, Q., Zhang, P., Zhou, Y., Zhan, X., & Zhang, G. (2016). RES-Scanner: A software package for genome-wide identification of RNA-editing sites. Gigaence, 5, 37.

    Google Scholar 

  52. Sun, Y., Li, X., Wu, D., Pan, Q., Ji, Y., Ren, H., & Ding, K. (2016). RED: A java-MySQL software for identifying and visualizing RNA editing sites using rule-based and statistical filters. PLoS ONE. https://doi.org/10.1371/journal.pone.0150465

    Article  PubMed  PubMed Central  Google Scholar 

  53. Zhang, F., Lu, Y. L., Yan, S. J., Xing, Q. H., & Tian, W. D. (2017). SPRINT: An SNP-free toolkit for identifying RNA editing sites. Bioinformatics, 33, 3538–3548.

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Wu, S., Liu, W., Aljohi, H. A., Alromaih, S. A., AlAnazi, I. O., Lin, Q., Yu, J., & Hu, S. (2018). REDO: RNA editing detection in plant organelles based on variant calling results. Journal Of Computational Biology, 25, 509–516.

    CAS  PubMed  Google Scholar 

  55. Picardi, E., Regina, T. M. R., Brennicke, A., & Quagliariello, C. (2007). REDIdb: The RNA editing database. Nucleic Acids Research, 35, D173–D177.

    CAS  PubMed  Google Scholar 

  56. Li, M., Xia, L., Zhang, Y. S., Niu, G. Y., Li, M. W., Wang, P., Zhang, Y., Sang, J., Zou, D., Hu, S. N., Hao, L. L., & Zhang, Z. (2019). Plant editosome database: A curated database of RNA editosome in plants. Nucleic Acids Research, 47, D170–D174.

    CAS  PubMed  Google Scholar 

  57. He, T., Du, P. F., & Li, Y. D. (2007). dbRES: A web-oriented database for annotated RNA editing sites. Nucleic Acids Research, 35, D141–D144.

    CAS  PubMed  Google Scholar 

  58. Yura, K., Sulaiman, S., Hatta, Y., Shionyu, M., & Go, M. (2009). RESOPS: A database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures. Plant And Cell Physiology, 50, 1865–1873.

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Xing, H.-L., Dong, L., Wang, Z.-P., Zhang, H.-Y., Han, C.-Y., Liu, B., Wang, X.-C., & Chen, Q.-J. (2014). A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biology, 14, 1–12.

    Google Scholar 

  60. Parker, M. T., Knop, K., Sherwood, A. V., Schurch, N. J., & Simpson, G. G. (2020). Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification. eLife Sciences, 9, e49658.

    CAS  Google Scholar 

  61. Small, I. D., Schallenberg-Rudinger, M., Takenaka, M., Mireau, H., & Ostersetzer-Biran, O. (2020). Plant organellar RNA editing: What 30 years of research has revealed. Plant Journal, 101, 1040–1056.

    CAS  Google Scholar 

  62. Hayes, M. L., & Santibanez, P. I. (2020). A plant pentatricopeptide repeat protein with a DYW-deaminase domain is sufficient for catalyzing C-to-U RNA editing in vitro. Journal of Biological Chemistry. https://doi.org/10.1074/jbc.RA119.011790

    Article  PubMed  PubMed Central  Google Scholar 

  63. Wang, Z. J., Lian, J. M., Li, Q. Y., Zhang, P., Zhou, Y., Zhan, X. Y., & Zhang, G. J. (2016). RES-Scanner: A software package for genome-wide identification of RNA-editing sites. GigaScience, 5, 9.

    Google Scholar 

Download references

Acknowledgements

This work was supported by the National Natural Science Foundation of China (U1812403-1，82073960 and 82274045), the National Science and Technology Fundamental Resources Investigation Program of China (2018FY100701), the Open Fund of State Key Laboratory of Southwestern Chinese Medicine Resources (SKLTCM2022015), Beijing Natural Scientific Foundation (7202135) and CAMS Innovation Fund for Medical Sciences (CIFMS, 2022-I2M-1-017).

Author information

Authors and Affiliations

  1. Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China

    Huihui Zhang, Yan Zheng, Guoshuai Zhang, Yujing Miao, Chang Liu & Linfang Huang

  2. Jiangxi University of Chinese Medicine, Nanchang, 330000, Jiangxi, China

    Huihui Zhang & Yan Zheng

Authors
  1. Huihui Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yan Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Guoshuai Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yujing Miao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chang Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Linfang Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Chang Liu or Linfang Huang.

Ethics declarations

Conflict of interest

The authors declare no competing financial interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 334 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhang, H., Zheng, Y., Zhang, G. et al. A Bibliometric Study for Plant RNA Editing Research: Trends and Future Challenges. Mol Biotechnol 65, 1207–1227 (2023). https://doi.org/10.1007/s12033-022-00641-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12033-022-00641-7

Keywords

Search

Navigation