{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T02:08:29Z","timestamp":1772071709093,"version":"3.50.1"},"reference-count":80,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2016,8,2]],"date-time":"2016-08-02T00:00:00Z","timestamp":1470096000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31271310"],"award-info":[{"award-number":["31271310"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Journal"],"published-print":{"date-parts":[[2016,9]]},"abstract":"<jats:title>Summary<\/jats:title><jats:p>Centromeres on eukaryotic chromosomes consist of large arrays of <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> repeats that undergo very rapid evolution. <jats:italic>Nelumbo nucifera<\/jats:italic> Gaertn. (sacred lotus) is a phylogenetic relict and an aquatic perennial basal eudicot. Studies concerning the centromeres of this basal eudicot species could provide ancient evolutionary perspectives. In this study, we characterized the centromeric marker protein NnCenH3 (sacred lotus centromere\u2010specific histone H3 variant), and used a chromatin immunoprecipitation (Ch<jats:styled-content style=\"fixed-case\">IP<\/jats:styled-content>)\u2010based technique to recover the NnCenH3 nucleosome\u2010associated sequences of sacred lotus. The properties of the centromere\u2010binding protein and <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> sequences revealed notable divergence between sacred lotus and other flowering plants, including the following factors: (i) an NnCenH3 alternative splicing variant comprising only a partial centromere\u2010targeting domain, (ii) active genes with low transcription levels in the NnCenH3 nucleosomal regions, and (iii) the prevalence of the Ty1\/<jats:italic>copia<\/jats:italic> class of long terminal repeat (<jats:styled-content style=\"fixed-case\">LTR<\/jats:styled-content>) retrotransposons in the centromeres of sacred lotus chromosomes. In addition, the dynamic natures of the centromeric region showed that some of the centromeric repeat <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> sequences originated from telomeric repeats, and a pair of centromeres on the dicentric chromosome\u00a01 was inactive in the metaphase cells of sacred lotus. Our characterization of the properties of centromeric <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> structure within the sacred lotus genome describes a centromeric profile in ancient basal eudicots and might provide evidence of the origins and evolution of centromeres. Furthermore, the identification of centromeric <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> sequences is of great significance for the assembly of the sacred lotus genome.<\/jats:p>","DOI":"10.1111\/tpj.13219","type":"journal-article","created":{"date-parts":[[2016,5,26]],"date-time":"2016-05-26T14:38:44Z","timestamp":1464273524000},"page":"568-582","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["The NnCenH3 protein and centromeric <scp>DNA<\/scp> sequence profiles of <i>Nelumbo nucifera<\/i> Gaertn. (sacred lotus) reveal the <scp>DNA<\/scp> structures and dynamics of centromeres in basal eudicots"],"prefix":"10.1111","volume":"87","author":[{"given":"Zhixuan","family":"Zhu","sequence":"first","affiliation":[{"name":"Department of Genetics State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan 430072 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Songtao","family":"Gui","sequence":"additional","affiliation":[{"name":"Department of Genetics State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan 430072 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Jin","sequence":"additional","affiliation":[{"name":"Department of Genetics State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan 430072 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rong","family":"Yi","sequence":"additional","affiliation":[{"name":"Department of Genetics State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan 430072 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhihua","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Genetics State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan 430072 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qian","family":"Qian","sequence":"additional","affiliation":[{"name":"Department of Genetics State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan 430072 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Ding","sequence":"additional","affiliation":[{"name":"Department of Genetics State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan 430072 China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2016,8,2]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.111278.110"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1241089"},{"issue":"1","key":"e_1_2_6_4_1","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1242\/jcs.100.1.219","article-title":"Localization of centromeric satellite and telomeric DNA sequences in dorsal root ganglion neurons, in\u00a0vitro","volume":"100","author":"Billia F.","year":"1991","journal-title":"J. Cell Sci."},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature02766"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2006.12.018"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1023\/A:1005797222148"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M111857200"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddi008"},{"key":"e_1_2_6_10_1","doi-asserted-by":"publisher","DOI":"10.1023\/A:1009280425125"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/aob\/mcu178"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncb2805"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2009.02.039"},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1303944110"},{"key":"e_1_2_6_15_1","doi-asserted-by":"publisher","DOI":"10.1159\/000437008"},{"key":"e_1_2_6_16_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.090013497"},{"key":"e_1_2_6_17_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.112.100511"},{"key":"e_1_2_6_18_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10577-012-9332-x"},{"key":"e_1_2_6_19_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1062939"},{"key":"e_1_2_6_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp208"},{"key":"e_1_2_6_21_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2229-10-204"},{"key":"e_1_2_6_22_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.018937"},{"key":"e_1_2_6_23_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.106.063628"},{"key":"e_1_2_6_24_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005494"},{"key":"e_1_2_6_25_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003209"},{"key":"e_1_2_6_26_1","doi-asserted-by":"publisher","DOI":"10.1007\/s001220051694"},{"key":"e_1_2_6_27_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12041-012-0181-3"},{"key":"e_1_2_6_28_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.12086"},{"key":"e_1_2_6_29_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00412-008-0161-9"},{"key":"e_1_2_6_30_1","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.201412011"},{"key":"e_1_2_6_31_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-12-r173"},{"key":"e_1_2_6_32_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0035261"},{"key":"e_1_2_6_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2009.08.036"},{"key":"e_1_2_6_34_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.242603899"},{"key":"e_1_2_6_35_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00438-010-0553-4"},{"key":"e_1_2_6_36_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2013-14-1-r10"},{"key":"e_1_2_6_37_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/150.4.1615"},{"key":"e_1_2_6_38_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2013-14-5-r41"},{"key":"e_1_2_6_39_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11103-010-9723-3"},{"key":"e_1_2_6_40_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msi069"},{"key":"e_1_2_6_41_1","doi-asserted-by":"publisher","DOI":"10.1186\/1759-8753-2-4"},{"key":"e_1_2_6_42_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-378"},{"key":"e_1_2_6_43_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt054"},{"key":"e_1_2_6_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1046-2023(03)00090-2"},{"key":"e_1_2_6_45_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh099"},{"key":"e_1_2_6_46_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.270.5242.1591"},{"key":"e_1_2_6_47_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature10158"},{"key":"e_1_2_6_48_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-313x.1998.00341.x"},{"key":"e_1_2_6_49_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn223"},{"key":"e_1_2_6_50_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.110.120337"},{"key":"e_1_2_6_51_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng1543"},{"key":"e_1_2_6_52_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.yexcr.2004.09.001"},{"key":"e_1_2_6_53_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2072"},{"key":"e_1_2_6_54_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.93.4.1443"},{"key":"e_1_2_6_55_1","volume-title":"RepeatMasker 4.0","author":"Smit A.","year":"2013"},{"key":"e_1_2_6_56_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10577-011-9208-5"},{"key":"e_1_2_6_57_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature10258"},{"key":"e_1_2_6_58_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.010425"},{"key":"e_1_2_6_59_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00412-004-0297-1"},{"key":"e_1_2_6_60_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0407154101"},{"key":"e_1_2_6_61_1","doi-asserted-by":"publisher","DOI":"10.1534\/g3.111.000125"},{"key":"e_1_2_6_62_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF00299145"},{"key":"e_1_2_6_63_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrm3107"},{"key":"e_1_2_6_64_1","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.22.21.7553-7561.2002"},{"key":"e_1_2_6_65_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0703808104"},{"key":"e_1_2_6_66_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00412-011-0315-z"},{"key":"e_1_2_6_67_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.12313"},{"key":"e_1_2_6_68_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.160887.113"},{"key":"e_1_2_6_69_1","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bav023"},{"key":"e_1_2_6_70_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10577-009-9029-y"},{"key":"e_1_2_6_71_1","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a015818"},{"key":"e_1_2_6_72_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000743"},{"key":"e_1_2_6_73_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.019273"},{"key":"e_1_2_6_74_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-014-0289-0"},{"key":"e_1_2_6_75_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2148-14-100"},{"key":"e_1_2_6_76_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.105.037945"},{"key":"e_1_2_6_77_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.106.043794"},{"key":"e_1_2_6_78_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0060286"},{"key":"e_1_2_6_79_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2229-10-178"},{"key":"e_1_2_6_80_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.13235"},{"key":"e_1_2_6_81_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF00357684"}],"container-title":["The Plant Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1111%2Ftpj.13219","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/tpj.13219","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,16]],"date-time":"2023-09-16T17:58:48Z","timestamp":1694887128000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/tpj.13219"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8,2]]},"references-count":80,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2016,9]]}},"alternative-id":["10.1111\/tpj.13219"],"URL":"https:\/\/doi.org\/10.1111\/tpj.13219","archive":["Portico"],"relation":{},"ISSN":["0960-7412","1365-313X"],"issn-type":[{"value":"0960-7412","type":"print"},{"value":"1365-313X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,8,2]]},"assertion":[{"value":"2016-02-02","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-05-23","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-08-02","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}