{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T23:59:10Z","timestamp":1790294350391,"version":"4.1.0"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T00:00:00Z","timestamp":1777852800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the French National Research Agency","award":["ANR-23-CE20-0038"],"award-info":[{"award-number":["ANR-23-CE20-0038"]}],"id":[{"id":"https:\/\/ror.org\/00rbzpz17","id-type":"ROR","asserted-by":"crossref"}]},{"name":"the \u00c9cole Universitaire de Recherche (EUR) TULIP-GS","award":["ANR-18-EURE-0019"],"award-info":[{"award-number":["ANR-18-EURE-0019"]}]},{"name":"the Laboratoires d\u2019Excellence (LABEX) TULIP","award":["ANR-10-LABX-41"],"award-info":[{"award-number":["ANR-10-LABX-41"]}]},{"DOI":"10.13039\/501100004223","name":"UPVD","doi-asserted-by":"publisher","award":["BQR-2022"],"award-info":[{"award-number":["BQR-2022"]}],"id":[{"id":"10.13039\/501100004223","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CIRAD Montpellier UMR AGAP Team Seapag and Team MEAC at LGDP"},{"name":"the \u2018Collectivit\u00e9 de Corse\u2019","id":[{"id":"https:\/\/ror.org\/05wyma827","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Doctoral school ED 305 from UPVD"},{"name":"Allocation Doctorale Occitanie","award":["2022-25 Save-Citrus"],"award-info":[{"award-number":["2022-25 Save-Citrus"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>DNA methylation plays a central role in the regulation of gene expression. In plants, methylation occurs in the CG, CHG, and CHH contexts, via distinct DNA methyltransferases including MET1, CMT3, and the RNA-directed DNA methylation (RdDM) pathway via DRM2. In interspecific hybrids, these epigenetic mechanisms are confronted to a mixed small RNA population and two subgenomes harbouring specific methylation patterns, therefore generating unique expression profiles. The aim of this work was to understand these regulations by analysing gene expression, DNA methylation, and small RNAs in a citrus hybrid resulting from the cross between Citrus reticulata (mandarin) and Citrus australasica (finger lime). Haplotype-resolved subgenomes assembly identified hundreds of allele-specifically expressed genes. Asymmetric reprogramming of methylation was observed, in particular an increase in CHH in C. australasica haplotype. Surprisingly, CHH methylation, usually associated with gene silencing, was correlated here with increased expression, but also 24\u00a0nt small RNA populations at their promoter regions. Similar analyses of the parental lines and other Citrus species suggest the correlation between CHH methylation-enriched promoter and high expression level is not due to the hybridization, but seem to be generally true for all citrus. These observations suggest that, in citrus fruit, RdDM is associated with higher transcriptional activity. This work also provides a full pipeline to analyse the expression profiles and DNA methylation in complex hybrids, which could be crucial for anticipating varieties resistant to diseases and the current threats affecting citriculture, such as the Huanglongbing disease.<\/jats:p>","DOI":"10.1093\/hr\/uhag183","type":"journal-article","created":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T11:59:57Z","timestamp":1777377597000},"source":"Crossref","is-referenced-by-count":0,"title":["Investigation of allele-specific expression in citrus hybrids reveals the association between siRNA-mediated\n                    <i>de novo<\/i>\n                    methylation and high expression in citrus genomes"],"prefix":"10.1093","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-2255-7489","authenticated-orcid":false,"given":"Khadidiatou","family":"Diop","sequence":"first","affiliation":[{"name":"CNRS\/UPVD, Plant Genome and Development (LGDP) , Perpignan 66100 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1533-5052","authenticated-orcid":false,"given":"Marie","family":"Bonnin","sequence":"additional","affiliation":[{"name":"CNRS\/UPVD, Plant Genome and Development (LGDP) , Perpignan 66100 ,","place":["France"]},{"name":"CNRS, Equipe d\u2019Adaptation des V\u00e9g\u00e9taux aux Changements Globaux, Projet Ressources Naturelles, UMR 6134 SPE, Univ de Corse , Corsica ,","place":["France"]},{"name":"UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana\u00efs","family":"Gibert","sequence":"additional","affiliation":[{"name":"CNRS\/UPVD, Plant Genome and Development (LGDP) , Perpignan 66100 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christel","family":"Llauro","sequence":"additional","affiliation":[{"name":"CNRS\/UPVD, Plant Genome and Development (LGDP) , Perpignan 66100 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yann","family":"Froelicher","sequence":"additional","affiliation":[{"name":"UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier ,","place":["France"]},{"name":"CIRAD, UMR AGAP Institut , F-20230 San Giuliano ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3515-2122","authenticated-orcid":false,"given":"Barbara","family":"Hufnagel","sequence":"additional","affiliation":[{"name":"UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier ,","place":["France"]},{"name":"CIRAD, UMR AGAP Institut , F-97170 Petit-Bourg, Guadeloupe ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2770-9688","authenticated-orcid":false,"given":"Nathalie","family":"Picault","sequence":"additional","affiliation":[{"name":"CNRS\/UPVD, Plant Genome and Development (LGDP) , Perpignan 66100 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2913-4104","authenticated-orcid":false,"given":"Fr\u00e9d\u00e9ric","family":"Pontvianne","sequence":"additional","affiliation":[{"name":"CNRS\/UPVD, Plant Genome and Development (LGDP) , Perpignan 66100 ,","place":["France"]},{"name":"iGReD, Universit\u00e9 Clermont Auvergne, CNRS, INSERM , 63001 Clermont-Ferrand ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,4]]},"reference":[{"key":"2026092419120653600_ref1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/978-3-031-51272-8_4","volume-title":"Sustainable Development of the Agrarian Economy Based on Digital Technologies and Smart Innovations","author":"Mukhametzyanov","year":"2024"},{"key":"2026092419120653600_ref2","volume-title":"Citrus Productions","author":"Curk","year":"2022"},{"key":"2026092419120653600_ref3","volume-title":"The Genus Citrus","author":"Ollitrault","year":"2020"},{"key":"2026092419120653600_ref4","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/nature25447","article-title":"Genomics of the origin and evolution of 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