Cargando…
Non-coding RNAs in the interaction between rice and Meloidogyne graminicola
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 va...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8293575/ https://www.ncbi.nlm.nih.gov/pubmed/34284724 http://dx.doi.org/10.1186/s12864-021-07735-7 |
_version_ | 1783725070356578304 |
---|---|
author | Verstraeten, Bruno Atighi, Mohammad Reza Ruiz-Ferrer, Virginia Escobar, Carolina De Meyer, Tim Kyndt, Tina |
author_facet | Verstraeten, Bruno Atighi, Mohammad Reza Ruiz-Ferrer, Virginia Escobar, Carolina De Meyer, Tim Kyndt, Tina |
author_sort | Verstraeten, Bruno |
collection | PubMed |
description | 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07735-7. |
format | Online Article Text |
id | pubmed-8293575 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-82935752021-07-21 Non-coding RNAs in the interaction between rice and Meloidogyne graminicola Verstraeten, Bruno Atighi, Mohammad Reza Ruiz-Ferrer, Virginia Escobar, Carolina De Meyer, Tim Kyndt, Tina BMC Genomics Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07735-7. BioMed Central 2021-07-20 /pmc/articles/PMC8293575/ /pubmed/34284724 http://dx.doi.org/10.1186/s12864-021-07735-7 Text en © The Author(s) 2021, corrected publication 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Verstraeten, Bruno Atighi, Mohammad Reza Ruiz-Ferrer, Virginia Escobar, Carolina De Meyer, Tim Kyndt, Tina Non-coding RNAs in the interaction between rice and Meloidogyne graminicola |
title | Non-coding RNAs in the interaction between rice and Meloidogyne graminicola |
title_full | Non-coding RNAs in the interaction between rice and Meloidogyne graminicola |
title_fullStr | Non-coding RNAs in the interaction between rice and Meloidogyne graminicola |
title_full_unstemmed | Non-coding RNAs in the interaction between rice and Meloidogyne graminicola |
title_short | Non-coding RNAs in the interaction between rice and Meloidogyne graminicola |
title_sort | non-coding rnas in the interaction between rice and meloidogyne graminicola |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8293575/ https://www.ncbi.nlm.nih.gov/pubmed/34284724 http://dx.doi.org/10.1186/s12864-021-07735-7 |
work_keys_str_mv | AT verstraetenbruno noncodingrnasintheinteractionbetweenriceandmeloidogynegraminicola AT atighimohammadreza noncodingrnasintheinteractionbetweenriceandmeloidogynegraminicola AT ruizferrervirginia noncodingrnasintheinteractionbetweenriceandmeloidogynegraminicola AT escobarcarolina noncodingrnasintheinteractionbetweenriceandmeloidogynegraminicola AT demeyertim noncodingrnasintheinteractionbetweenriceandmeloidogynegraminicola AT kyndttina noncodingrnasintheinteractionbetweenriceandmeloidogynegraminicola |