Academic Bibliography

 Search 200 years of publications by Ghent University researchers.
Advanced search
1 file | 1.54 MB
Add to list
  1. Search results
  2. Non-coding RNAs in the interaction be...

Non-coding RNAs in the interaction between rice and Meloidogyne graminicola

Bruno Verstraeten (UGent) , Mohammad Atighi Quchan Atigh, Virginia Ruiz-Ferrer, Carolina Escobar, Tim De Meyer (UGent) and Tina Kyndt (UGent)
(2021) BMC GENOMICS. 22(1).
Author
Organization
Project
Abstract
Background Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of various plant processes, elucidating their regulation during this interaction may lead to new strategies to improve crop protection. In this study, we aimed to identify and characterize rice siRNAs, miRNAs and lncRNAs responsive to early infection with RKN Meloidogyne graminicola (Mg), based on sequencing of small RNA, degradome and total RNA libraries from rice gall tissues compared with uninfected root tissues. Results We found 425 lncRNAs, 3739 siRNAs and 16 miRNAs to be differentially expressed between both tissues, of which a subset was independently validated with RT-qPCR. Functional prediction of the lncRNAs indicates that a large part of their potential target genes code for serine/threonine protein kinases and transcription factors. Differentially expressed siRNAs have a predominant size of 24 nts, suggesting a role in DNA methylation. Differentially expressed miRNAs are generally downregulated and target transcription factors, which show reduced degradation according to the degradome data. Conclusions To our knowledge, this work is the first to focus on small and long non-coding RNAs in the interaction between rice and Mg, and provides an overview of rice non-coding RNAs with the potential to be used as a resource for the development of new crop protection strategies.
Keywords
Non-coding RNAs, Epigenetics, siRNAs, miRNAs, lncRNAs, Nematode, Oryza sativa, DIRECTED DNA METHYLATION, DROUGHT TOLERANCE, GRAIN-YIELD, ROOT-KNOT, EPIGENETIC PATHWAY, PLANT DEVELOPMENT, R-PACKAGE, ARABIDOPSIS, RESISTANCE, EXPRESSION

Downloads

  • Download
    Non-coding RNAs.pdf
    • full text (Published version)
    • |
    • open access
    • |
    • PDF
    • |
    • 1.54 MB

Citation

Please use this url to cite or link to this publication:

MLA
Verstraeten, Bruno, et al. “Non-Coding RNAs in the Interaction between Rice and Meloidogyne Graminicola.” BMC GENOMICS, vol. 22, no. 1, 2021, doi:10.1186/s12864-021-07735-7.
APA
Verstraeten, B., Atighi Quchan Atigh, M., Ruiz-Ferrer, V., Escobar, C., De Meyer, T., & Kyndt, T. (2021). Non-coding RNAs in the interaction between rice and Meloidogyne graminicola. BMC GENOMICS, 22(1). https://doi.org/10.1186/s12864-021-07735-7
Chicago author-date
Verstraeten, Bruno, Mohammad Atighi Quchan Atigh, Virginia Ruiz-Ferrer, Carolina Escobar, Tim De Meyer, and Tina Kyndt. 2021. “Non-Coding RNAs in the Interaction between Rice and Meloidogyne Graminicola.” BMC GENOMICS 22 (1). https://doi.org/10.1186/s12864-021-07735-7.
Chicago author-date (all authors)
Verstraeten, Bruno, Mohammad Atighi Quchan Atigh, Virginia Ruiz-Ferrer, Carolina Escobar, Tim De Meyer, and Tina Kyndt. 2021. “Non-Coding RNAs in the Interaction between Rice and Meloidogyne Graminicola.” BMC GENOMICS 22 (1). doi:10.1186/s12864-021-07735-7.
Vancouver
1.
Verstraeten B, Atighi Quchan Atigh M, Ruiz-Ferrer V, Escobar C, De Meyer T, Kyndt T. Non-coding RNAs in the interaction between rice and Meloidogyne graminicola. BMC GENOMICS. 2021;22(1).
IEEE
[1]
B. Verstraeten, M. Atighi Quchan Atigh, V. Ruiz-Ferrer, C. Escobar, T. De Meyer, and T. Kyndt, “Non-coding RNAs in the interaction between rice and Meloidogyne graminicola,” BMC GENOMICS, vol. 22, no. 1, 2021.
@article{8741081,
  abstract     = {{Background Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of various plant processes, elucidating their regulation during this interaction may lead to new strategies to improve crop protection. In this study, we aimed to identify and characterize rice siRNAs, miRNAs and lncRNAs responsive to early infection with RKN Meloidogyne graminicola (Mg), based on sequencing of small RNA, degradome and total RNA libraries from rice gall tissues compared with uninfected root tissues. Results We found 425 lncRNAs, 3739 siRNAs and 16 miRNAs to be differentially expressed between both tissues, of which a subset was independently validated with RT-qPCR. Functional prediction of the lncRNAs indicates that a large part of their potential target genes code for serine/threonine protein kinases and transcription factors. Differentially expressed siRNAs have a predominant size of 24 nts, suggesting a role in DNA methylation. Differentially expressed miRNAs are generally downregulated and target transcription factors, which show reduced degradation according to the degradome data. Conclusions To our knowledge, this work is the first to focus on small and long non-coding RNAs in the interaction between rice and Mg, and provides an overview of rice non-coding RNAs with the potential to be used as a resource for the development of new crop protection strategies.}},
  articleno    = {{560}},
  author       = {{Verstraeten, Bruno and Atighi Quchan Atigh, Mohammad and Ruiz-Ferrer, Virginia and Escobar, Carolina and De Meyer, Tim and Kyndt, Tina}},
  issn         = {{1471-2164}},
  journal      = {{BMC GENOMICS}},
  keywords     = {{Non-coding RNAs,Epigenetics,siRNAs,miRNAs,lncRNAs,Nematode,Oryza sativa,DIRECTED DNA METHYLATION,DROUGHT TOLERANCE,GRAIN-YIELD,ROOT-KNOT,EPIGENETIC PATHWAY,PLANT DEVELOPMENT,R-PACKAGE,ARABIDOPSIS,RESISTANCE,EXPRESSION}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{19}},
  title        = {{Non-coding RNAs in the interaction between rice and Meloidogyne graminicola}},
  url          = {{http://doi.org/10.1186/s12864-021-07735-7}},
  volume       = {{22}},
  year         = {{2021}},
}
Altmetric
View in Altmetric
Web of Science
Times cited: