{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T07:45:13Z","timestamp":1792050313645,"version":"4.4.0"},"reference-count":84,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["nph.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["New Phytologist"],"published-print":{"date-parts":[[2026,11]]},"abstract":"<jats:title>Summary<\/jats:title>\n                  <jats:p>\n                    <jats:list list-type=\"bullet\">\n                      <jats:list-item>\n                        <jats:p>Genetic variations accumulate over long evolutionary timescales, whereas epigenetic modifications can arise rapidly and be inherited across generations. However, the interplay between genetic and epigenetic variations in shaping ecotype\u2010specific phenotypic plasticity remains elusive.<\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>Focusing on two lotus ecotypes that evolved under distinct winter temperature regions and display divergent annual growth cycles under cold stress, we generated DNA methylation landscapes across three sequence contexts (CG, CHG, and CHH, where H\u2009=\u2009A, T, or C) and identified single\u2010cytosine methylation polymorphisms (SMPs) and single\u2010nucleotide polymorphisms (SNPs). Interestingly, only CG methylation patterns mirror population\u2010level genetic variations.<\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>\n                          Using epigenetic genome\u2010wide association analysis, we identified differentially methylated CG sites that are either\n                          <jats:italic>cis<\/jats:italic>\n                          \u2010 or\n                          <jats:italic>trans<\/jats:italic>\n                          \u2010regulated by SNP. Notably, we constructed a multifactorial regulatory network centered on the\n                          <jats:italic>NnMKK4<\/jats:italic>\n                          \u2010\n                          <jats:italic>NnCYCD5<\/jats:italic>\n                          module, linking cold response with cell cycle regulation. Temperature stress experiments conducted on lotus ecotypes and transgenic Arabidopsis (OE\u2010\n                          <jats:italic>NnMKK4<\/jats:italic>\n                          and OE\u2010\n                          <jats:italic>NnCYCD5<\/jats:italic>\n                          ) confirmed that\n                          <jats:italic>NnMKK4<\/jats:italic>\n                          acts as a cold receptor and that\n                          <jats:italic>NnCYCD5<\/jats:italic>\n                          promotes cell cycle progression and growth under cold conditions.\n                        <\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>Collectively, our findings provide novel insights into the co\u2010evolutionary dynamics of epigenetic and genetic variations that are associated with different growth cycles of lotus ecotypes in response to cold stress.<\/jats:p>\n                      <\/jats:list-item>\n                    <\/jats:list>\n                  <\/jats:p>","DOI":"10.1111\/nph.71570","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T05:51:49Z","timestamp":1789624309000},"page":"1510-1525","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Unraveling epigenetic and genetic variations in response to cold stress in two lotus ecotypes"],"prefix":"10.1111","volume":"252","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2674-0341","authenticated-orcid":false,"given":"Yue","family":"Zhang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops Wuhan Botanical Garden, Chinese Academy of Sciences  Wuhan 430074 China"},{"name":"Hubei Key Laboratory of Wetland Evolution &amp; Ecological Restoration Wuhan Botanical Garden, Chinese Academy of Sciences  Wuhan 430074 China"},{"name":"Department of Plant Biotechnology and Bioinformatics Ghent University  Ghent 9052 Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2277-005X","authenticated-orcid":false,"given":"Xiangyan","family":"He","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops Wuhan Botanical Garden, Chinese Academy of Sciences  Wuhan 430074 China"},{"name":"Hubei Key Laboratory of Wetland Evolution &amp; Ecological Restoration Wuhan Botanical Garden, Chinese Academy of Sciences  Wuhan 430074 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1907-3552","authenticated-orcid":false,"given":"Tao","family":"Shi","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops Wuhan Botanical Garden, Chinese Academy of Sciences  Wuhan 430074 China"},{"name":"Hubei Key Laboratory of Wetland Evolution &amp; Ecological Restoration Wuhan Botanical Garden, Chinese Academy of Sciences  Wuhan 430074 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8920-9270","authenticated-orcid":false,"given":"Zhen","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics Ghent University  Ghent 9052 Belgium"},{"name":"VIB Center for Plant Systems Biology  Ghent 9052 Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3425-5939","authenticated-orcid":false,"given":"Jinming","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops Wuhan Botanical Garden, Chinese Academy of Sciences  Wuhan 430074 China"},{"name":"Hubei Key Laboratory of Wetland Evolution &amp; Ecological Restoration Wuhan Botanical Garden, Chinese Academy of Sciences  Wuhan 430074 China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2020.08.011"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2012-13-10-r87"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.094052.109"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.15408"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.16658"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1080\/15592294.2019.1625674"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pbi.2016.12.007"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature05913"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0960-9822(02)00925-9"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg1601"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2023.09.010"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/ert451"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1248127"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.1501340"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1111\/brv.12453"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.15689"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.18225"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1209329109"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.113.114793"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2021.03.005"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2009.06.015"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13522"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1010452"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx595"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.19265"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2018.09.007"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-021-00969-x"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.14421"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2120-7"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1111\/jipb.12606"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.15252\/embj.201488883"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng1089"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx240"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.177659.114"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac137"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0201-4"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.15933"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-021-00828-8"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2019.12.007"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pbi.2011.01.003"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.15029"},{"key":"e_1_2_9_44_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-021-00407-y"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0408-0"},{"key":"e_1_2_9_46_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8"},{"key":"e_1_2_9_47_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.16220"},{"key":"e_1_2_9_48_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02381-4"},{"key":"e_1_2_9_49_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2021.06.001"},{"key":"e_1_2_9_50_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.18.00074"},{"key":"e_1_2_9_51_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.14370"},{"key":"e_1_2_9_52_1","doi-asserted-by":"publisher","DOI":"10.1101\/2023.07.16.549253"},{"key":"e_1_2_9_53_1","doi-asserted-by":"publisher","DOI":"10.1093\/plcell\/koac006"},{"key":"e_1_2_9_54_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"e_1_2_9_55_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.112.104695"},{"key":"e_1_2_9_56_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-1059-0"},{"key":"e_1_2_9_57_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.18876"},{"key":"e_1_2_9_58_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msq150"},{"key":"e_1_2_9_59_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.15388"},{"key":"e_1_2_9_60_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3122"},{"key":"e_1_2_9_61_1","volume-title":"R: a language and environment for statistical computing","author":"R Core Team","year":"2024"},{"key":"e_1_2_9_62_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/eraa088"},{"key":"e_1_2_9_63_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.15.01011"},{"key":"e_1_2_9_64_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-arplant-042809-112252"},{"key":"e_1_2_9_65_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.19464"},{"key":"e_1_2_9_66_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11968"},{"key":"e_1_2_9_67_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts163"},{"key":"e_1_2_9_68_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02161-6"},{"key":"e_1_2_9_69_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41477-025-02108-4"},{"key":"e_1_2_9_70_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.14080"},{"key":"e_1_2_9_71_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2341"},{"key":"e_1_2_9_72_1","first-page":"4.10.11","article-title":"Using RepeatMasker to identify repetitive elements in genomic sequences","volume":"4","author":"Tarailo\u2010Graovac M","year":"2009","journal-title":"Current Protocols in Bioinformatics"},{"key":"e_1_2_9_73_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg.2017.86"},{"key":"e_1_2_9_74_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-1127-5"},{"key":"e_1_2_9_75_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature20784"},{"key":"e_1_2_9_76_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-024-06266-7"},{"key":"e_1_2_9_77_1","doi-asserted-by":"publisher","DOI":"10.1093\/plphys\/kiad209"},{"key":"e_1_2_9_78_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19333-4"},{"key":"e_1_2_9_79_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tplants.2014.10.001"},{"key":"e_1_2_9_80_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep13059"},{"key":"e_1_2_9_81_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2019.12.012"},{"key":"e_1_2_9_82_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-018-0016-z"},{"key":"e_1_2_9_83_1","volume-title":"New lotus flower cultivars in China I","author":"Zhang XY","year":"2011"},{"key":"e_1_2_9_84_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-023-01743-7"},{"key":"e_1_2_9_85_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2017.09.024"}],"container-title":["New Phytologist"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/nph.onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/nph.71570","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/nph.onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/nph.71570","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/nph.onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/nph.71570","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T06:47:50Z","timestamp":1792046870000},"score":1,"resource":{"primary":{"URL":"https:\/\/nph.onlinelibrary.wiley.com\/doi\/10.1111\/nph.71570"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,16]]},"references-count":84,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,11]]}},"alternative-id":["10.1111\/nph.71570"],"URL":"https:\/\/doi.org\/10.1111\/nph.71570","archive":["Portico"],"relation":{},"ISSN":["0028-646X","1469-8137"],"issn-type":[{"value":"0028-646X","type":"print"},{"value":"1469-8137","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,16]]},"assertion":[{"value":"2026-01-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-25","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-16","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}