{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T10:02:17Z","timestamp":1790762537506,"version":"4.1.0"},"reference-count":49,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"vor","delay-in-days":2,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Evolution and Development"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Homeodomain transcription factors share an ancient helix\u2010turn\u2010helix DNA\u2010binding core yet regulate diverse developmental and reproductive programs across eukaryotes. We curated 355 nonredundant homeodomain structures spanning fungi, animals, and plants, including 118 experimental PDB entries and 237 high\u2010confidence AlphaFold2 models, and performed large\u2010scale structural comparisons using DaliLite5. Structural distances were summarized as a clustering tree visualized in iTOL and interpreted through topology\u2010guided PyMOL superpositions and sequence\u2010logo mapping of conserved positions. Across kingdoms, the canonical three\u2010helix HTH geometry and the recognition\u2010helix framework were strongly conserved, whereas structural diversification was concentrated in interhelical loops, terminal regions, linker segments, and lineage\u2010specific auxiliary modules. Fungal mating\u2010type homeodomains and major animal classes retained conserved recognition\u2010helix architecture despite sequence divergence, while plant WOX, ZF\u2010HD, PHD\u2010associated, and SAWADEE\u2010associated architectures illustrated modular expansion for developmental and chromatin\u2010context integration.<\/jats:p>","DOI":"10.1111\/ede.70059","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T07:04:13Z","timestamp":1788419053000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Cross\u2010Kingdom Structural Conservation and Diversification of Homeodomains Across Major Eukaryotic Lineages"],"prefix":"10.1111","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-4911-7742","authenticated-orcid":false,"given":"Gloria Elisabeth","family":"Buarante","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Faculty of Mathematics and Natural Sciences IPB University Bogor Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4017-0499","authenticated-orcid":false,"given":"Ema","family":"Damayanti","sequence":"additional","affiliation":[{"name":"Research Center for Food Technology and Processing, BRIN Yogyakarta Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9522-2129","authenticated-orcid":false,"given":"Popi Asri","family":"Kurniatin","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Faculty of Mathematics and Natural Sciences IPB University Bogor Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9861-1755","authenticated-orcid":false,"given":"Inda","family":"Setyawati","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Faculty of Mathematics and Natural Sciences IPB University Bogor Indonesia"},{"name":"Bioinformatics Study Program, Faculty of Mathematics and Natural Sciences IPB University Bogor Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0783-0483","authenticated-orcid":false,"given":"Rini","family":"Riffiani","sequence":"additional","affiliation":[{"name":"Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN) Cibinong Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,3]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-019-6080-8"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003160"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1101752108"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.15.3258"},{"key":"e_1_2_10_6_1","doi-asserted-by":"crossref","unstructured":"Banerjee\u2010Basu S. 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D.Baxevanis.2001. \u201cThe Homeodomain Resource: Sequences Structures DNA Binding Sites and Genomic Information.\u201dNucleic Acids Research29 no. 1: 291\u2013293.https:\/\/doi.org\/10.1093\/nar\/29.1.291.","DOI":"10.1093\/nar\/29.1.291"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.25.13749"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evy170"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.21.4173"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00412-015-0543-8"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03130-20"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1128\/aem.02208-23"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1128\/mmbr.62.1.55-70.1998"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.849004"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.3390\/plants2020317"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1995.0401"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad275"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.90.13.6360"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg563"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.bi.63.070194.002415"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz536"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-0270-6_3"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1012084"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(90)90453-L"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-47396-0"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1016\/J.MIB.2010.09.016"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.6.10.1467"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002195"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae268"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.3390\/genes13081481\/s1"},{"key":"e_1_2_10_31_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijbiomac.2025.144377"},{"key":"e_1_2_10_32_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.270.5234.262"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.1155\/2014\/534140"},{"key":"e_1_2_10_34_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jafc.3c07853"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1093\/NAR\/25.24.4940"},{"key":"e_1_2_10_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bap004"},{"key":"e_1_2_10_37_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp201"},{"key":"e_1_2_10_38_1","doi-asserted-by":"publisher","DOI":"10.1111\/pce.70272"},{"key":"e_1_2_10_39_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2008.05.023"},{"key":"e_1_2_10_40_1","doi-asserted-by":"publisher","DOI":"10.3390\/plants13213108"},{"key":"e_1_2_10_41_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2021.648765"},{"key":"e_1_2_10_42_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-16024-y"},{"key":"e_1_2_10_43_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.11.6228"},{"key":"e_1_2_10_44_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.105.070565"},{"key":"e_1_2_10_45_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1061"},{"key":"e_1_2_10_46_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi602657e"},{"key":"e_1_2_10_47_1","doi-asserted-by":"crossref","unstructured":"Wilson D. 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