Epigenomic response to insect herbivory in Lombardy poplar: assessing geographic variation in DNA methylation changes

[Data availability] The bisulfite sequencing raw data is deposited in the ENA Sequence Read Archive Repository (https://www.ebi.ac.uk/ena/) under study accession numbers PRJEB51853 (https://www.ebi.ac.uk/ena/browser/view/PRJEB51853) and PRJEB51623 (https://www.ebi.ac.uk/ena/browser/view/PRJEB51623)....

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Detalles Bibliográficos
Autores: Medrano, Mónica, Troyee, A. Niloya, Peña-Ponton, Cristian, Verhoeven, Koen J.F., Alonso, Conchita
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2026
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/423618
Acceso en línea:http://hdl.handle.net/10261/423618
https://api.elsevier.com/content/abstract/scopus_id/105029944877
Access Level:acceso abierto
Palabra clave:Reduced representation bisulfite sequencing
Biotic stress
Differentially methylated cytosines
Jasmonic acid
Lymantria dispar
Poplars
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oai_identifier_str oai:digital.csic.es:10261/423618
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Epigenomic response to insect herbivory in Lombardy poplar: assessing geographic variation in DNA methylation changes
title Epigenomic response to insect herbivory in Lombardy poplar: assessing geographic variation in DNA methylation changes
spellingShingle Epigenomic response to insect herbivory in Lombardy poplar: assessing geographic variation in DNA methylation changes
Medrano, Mónica
Reduced representation bisulfite sequencing
Biotic stress
Differentially methylated cytosines
Jasmonic acid
Lymantria dispar
Poplars
title_short Epigenomic response to insect herbivory in Lombardy poplar: assessing geographic variation in DNA methylation changes
title_full Epigenomic response to insect herbivory in Lombardy poplar: assessing geographic variation in DNA methylation changes
title_fullStr Epigenomic response to insect herbivory in Lombardy poplar: assessing geographic variation in DNA methylation changes
title_full_unstemmed Epigenomic response to insect herbivory in Lombardy poplar: assessing geographic variation in DNA methylation changes
title_sort Epigenomic response to insect herbivory in Lombardy poplar: assessing geographic variation in DNA methylation changes
dc.creator.none.fl_str_mv Medrano, Mónica
Troyee, A. Niloya
Peña-Ponton, Cristian
Verhoeven, Koen J.F.
Alonso, Conchita
author Medrano, Mónica
author_facet Medrano, Mónica
Troyee, A. Niloya
Peña-Ponton, Cristian
Verhoeven, Koen J.F.
Alonso, Conchita
author_role author
author2 Troyee, A. Niloya
Peña-Ponton, Cristian
Verhoeven, Koen J.F.
Alonso, Conchita
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Conferencia de Rectores de las Universidades Españolas
Consejo Superior de Investigaciones Científicas (España)
European Commission
Ministerio de Ciencia, Innovación y Universidades (España)
Agencia Estatal de Investigación (España)
Medrano, Mónica [0000-0002-2816-4192]
Troyee, A. Niloya [0000-0001-8134-0135]
Peña-Ponton, Cristian [0000-0003-0671-2124]
Verhoeven, Koen J.F. [0000-0003-3002-4102]
Alonso, Conchita [0000-0002-7418-3204]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Reduced representation bisulfite sequencing
Biotic stress
Differentially methylated cytosines
Jasmonic acid
Lymantria dispar
Poplars
topic Reduced representation bisulfite sequencing
Biotic stress
Differentially methylated cytosines
Jasmonic acid
Lymantria dispar
Poplars
description [Data availability] The bisulfite sequencing raw data is deposited in the ENA Sequence Read Archive Repository (https://www.ebi.ac.uk/ena/) under study accession numbers PRJEB51853 (https://www.ebi.ac.uk/ena/browser/view/PRJEB51853) and PRJEB51623 (https://www.ebi.ac.uk/ena/browser/view/PRJEB51623). The Populus nigra cv. ‘italica’ reference genome used is available also at ENA project PRJEB44889 (https://www.ebi.ac.uk/ena/browser/view/PRJEB44889). Extended methods (sample metadata; custom scripts, and other relevant data) will be given upon request from the corresponding author.
publishDate 2026
dc.date.none.fl_str_mv 2026
2026
2026
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/423618
https://api.elsevier.com/content/abstract/scopus_id/105029944877
url http://hdl.handle.net/10261/423618
https://api.elsevier.com/content/abstract/scopus_id/105029944877
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
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info:eu-repo/grantagreement/EC/H2020/764965
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-104365GB-I00
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2022-141530NB-C21
The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1007/s11295-025-01727-4
https://doi.org/10.1007/s11295-025-01727-4
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
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spelling Epigenomic response to insect herbivory in Lombardy poplar: assessing geographic variation in DNA methylation changesMedrano, MónicaTroyee, A. NiloyaPeña-Ponton, CristianVerhoeven, Koen J.F.Alonso, ConchitaReduced representation bisulfite sequencingBiotic stressDifferentially methylated cytosinesJasmonic acidLymantria disparPoplars[Data availability] The bisulfite sequencing raw data is deposited in the ENA Sequence Read Archive Repository (https://www.ebi.ac.uk/ena/) under study accession numbers PRJEB51853 (https://www.ebi.ac.uk/ena/browser/view/PRJEB51853) and PRJEB51623 (https://www.ebi.ac.uk/ena/browser/view/PRJEB51623). The Populus nigra cv. ‘italica’ reference genome used is available also at ENA project PRJEB44889 (https://www.ebi.ac.uk/ena/browser/view/PRJEB44889). Extended methods (sample metadata; custom scripts, and other relevant data) will be given upon request from the corresponding author.DNA methylation is a key epigenetic mechanism in plants, reported to be involved in regulating responses and local adaptation to abiotic and biotic stressors that could be particularly beneficial for long-lived tree species. Given that climate change is predicted to promote insect outbreaks, epigenetic studies of herbivory responses in trees may be vital for forest management and conservation. Here, we study changes in DNA methylation in response to herbivory in the clonal tree Populus nigra cv. ‘italica’ (Lombardy poplar). Cuttings were collected from three distant geographical locations (Spain, Italy, Poland), clonally replicated and grown in a common environment. We used reduced representation bisulfite sequencing to assess methylation changes between three experimental categories: (i) insect and (ii) artificial herbivory, and (iii) undamaged plants. Our results indicate that DNA methylation in poplars from different provenance, despite being genetically very similar, responded differently to experimental herbivory with plant origin accounting for 17.2% of the variation across CG, CHG, and CHH contexts. Both insect and artificial herbivory induced a significantly higher response in CHH context. When we explore loci with contrasting methylation levels (differentially methylated cytosines, DMCs), Spanish poplars were the most responsive to insect damage while Polish trees to artificial herbivory. DMCs were primarily located in gene bodies and their flanking regions (CG, CHG) or intergenic regions (CHH). Further, about one-third of DMCs obtained in CHH context were associated with transposable elements (TEs). Our findings suggest that for a better understanding of the role of the epigenetics in plant responses to herbivory we may need to take into account history of exposure, and highlight the importance of incorporating epigenetic knowledge to manage natural forests and tree plantations to help them cope with their environmental challenges.Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This work was supported and funded by the European Union’s Horizon 2020 research and innovation program via the Marie Sklodowska-Curie ITN ‘EpiDiverse’ (grant agreement No 764965) < https://cordis.europa.eu/project/id/764965 >. C.A. and M.M. were also supported by the Spanish Government through the Research Projects ‘Epinter’ (PID2019-104365 GB-I00) and ‘Distepic’ (PID2022-141530NB-C21, Ministerio de Ciencia e Innovación).Peer reviewedSpringer NatureConferencia de Rectores de las Universidades EspañolasConsejo Superior de Investigaciones Científicas (España)European CommissionMinisterio de Ciencia, Innovación y Universidades (España)Agencia Estatal de Investigación (España)Medrano, Mónica [0000-0002-2816-4192]Troyee, A. Niloya [0000-0001-8134-0135]Peña-Ponton, Cristian [0000-0003-0671-2124]Verhoeven, Koen J.F. [0000-0003-3002-4102]Alonso, Conchita [0000-0002-7418-3204]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202620262026info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/423618https://api.elsevier.com/content/abstract/scopus_id/105029944877reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantagreement/EC/H2020/764965info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-104365GB-I00info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2022-141530NB-C21The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1007/s11295-025-01727-4https://doi.org/10.1007/s11295-025-01727-4Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/4236182026-05-22T06:33:51Z
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