{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T10:54:50Z","timestamp":1790938490660,"version":"4.1.0"},"reference-count":49,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T00:00:00Z","timestamp":1790899200000},"content-version":"vor","delay-in-days":31,"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":["Physiologia Plantarum"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Fruit color is a crucial biological trait of apple and is closely correlated with its nutritional value. The coloration of apple fruit is primarily determined by the anthocyanin accumulation in the peel. Nevertheless, the molecular mechanisms underlying peel anthocyanin accumulation in apple remain poorly understood. In the present study, we updated the apple genome annotation, which provides a valuable resource for the identification of novel genes and further functional studies on apple peel coloration. Using RNA\u2010seq transcriptome analysis, we systematically characterized the regulatory mechanisms governing anthocyanin biosynthesis and color formation in apple. Particular attention was given to newly identified genes with potential regulatory roles in anthocyanin accumulation. By integrating mRNA and small RNA transcriptomic data, we uncovered a core miR858\u2010MdMYB regulatory module that participates in apple anthocyanin metabolism. Furthermore, comparative transcriptomic analysis revealed that the photosystem I center gene\n                    <jats:italic>MdPSAEA<\/jats:italic>\n                    is involved in the regulation of apple anthocyanin biosynthesis. Collectively, our study provides an updated genome annotation and offers novel insights into the molecular basis of anthocyanin accumulation in apple.\n                  <\/jats:p>","DOI":"10.1111\/ppl.71090","type":"journal-article","created":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T10:06:23Z","timestamp":1790935583000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Manually Annotated Gene Prediction of the Apple Genome and Identification of Anthocyanin Biosynthesis Mechanisms in Apple"],"prefix":"10.1111","volume":"178","author":[{"given":"Liwei","family":"Zheng","sequence":"first","affiliation":[{"name":"School of Agriculture and Biomanufacturing Zhengzhou University  Zhengzhou China"},{"name":"Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops  Zhengzhou China"},{"name":"Henan Funiu Mountain Biological and Ecological Environment Observatory  China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hangkai","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Agriculture and Biomanufacturing Zhengzhou University  Zhengzhou China"},{"name":"Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops  Zhengzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1541-0726","authenticated-orcid":false,"given":"Yingli","family":"Yang","sequence":"additional","affiliation":[{"name":"Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops  Zhengzhou China"},{"name":"Henan Funiu Mountain Biological and Ecological Environment Observatory  China"},{"name":"School of Life Sciences Zhengzhou University  Zhengzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yinglei","family":"Li","sequence":"additional","affiliation":[{"name":"School of Agriculture and Biomanufacturing Zhengzhou University  Zhengzhou China"},{"name":"Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops  Zhengzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junhan","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Life Sciences Zhengzhou University  Zhengzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Life Sciences Zhengzhou University  Zhengzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quanwei","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Life Sciences Zhengzhou University  Zhengzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengnan","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Life Sciences Zhengzhou University  Zhengzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-3643-8730","authenticated-orcid":false,"given":"Jinyong","family":"Huang","sequence":"additional","affiliation":[{"name":"Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops  Zhengzhou China"},{"name":"Henan Funiu Mountain Biological and Ecological Environment Observatory  China"},{"name":"School of Life Sciences Zhengzhou University  Zhengzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,2]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.plaphy.2016.06.032","article-title":"The Molecular Cloning and Functional Characterization of MdMYC2, A bHLH Transcription Factor in Apple","volume":"108","author":"An J.","year":"2016","journal-title":"Plant Physiology and 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Cultivar \u2018Ralls\u2019 and Its Blushed Sport","volume":"185","author":"Xu Y.","year":"2012","journal-title":"Euphytica"},{"key":"e_1_2_11_45_1","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1111\/pce.15271","article-title":"MsERF17 Promotes Ethylene\u2010Induced Anthocyanin Biosynthesis Under Drought Conditions in \n                     Malus spectabilis\n                   Leaves","volume":"48","author":"Xu Y.","year":"2025","journal-title":"Plant, Cell & Environment"},{"key":"e_1_2_11_46_1","doi-asserted-by":"crossref","first-page":"1683","DOI":"10.1111\/pbi.13839","article-title":"The MdBBX22\u2010miR858\u2010MdMYB9\/11\/12 Module Regulates Proanthocyanidin Biosynthesis in Apple Peel","volume":"20","author":"Zhang B.","year":"2022","journal-title":"Plant Biotechnology Journal"},{"key":"e_1_2_11_47_1","doi-asserted-by":"crossref","first-page":"112242","DOI":"10.1016\/j.scienta.2023.112242","article-title":"Manually Annotated Gene Prediction of the CN14 Peach Genome","volume":"321","author":"Zhang H.","year":"2023","journal-title":"Scientia Horticulturae"},{"key":"e_1_2_11_48_1","doi-asserted-by":"crossref","first-page":"koag139","DOI":"10.1093\/plcell\/koag139","article-title":"Chilling\u2010Responsive Strigolactone Signaling Orchestrates Bud Break and Chilling Tolerance in Apple","volume":"38","author":"Zhang Y.","year":"2026","journal-title":"Plant Cell"},{"key":"e_1_2_11_49_1","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1093\/plcell\/koad297","article-title":"The Transcription Factor MdBPC2 Alters Apple Growth and Promotes Dwarfing by Regulating Auxin Biosynthesis","volume":"36","author":"Zhao H.","year":"2024","journal-title":"Plant Cell"},{"key":"e_1_2_11_50_1","doi-asserted-by":"crossref","first-page":"koaf284","DOI":"10.1093\/plcell\/koaf284","article-title":"MdKIN10\u2010Mediated Phosphorylation of the E3 Ubiquitin Ligase MdMIEL1 Leads to Its Autophagic Degradation Under Cold Stress","volume":"38","author":"Zhi F.","year":"2026","journal-title":"Plant Cell"}],"container-title":["Physiologia Plantarum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/ppl.71090","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/ppl.71090","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/ppl.71090","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T10:06:36Z","timestamp":1790935596000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/ppl.71090"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":49,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["10.1111\/ppl.71090"],"URL":"https:\/\/doi.org\/10.1111\/ppl.71090","archive":["Portico"],"relation":{},"ISSN":["0031-9317","1399-3054"],"issn-type":[{"value":"0031-9317","type":"print"},{"value":"1399-3054","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"2026-03-28","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-13","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-10-02","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e71090"}}