{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T14:51:32Z","timestamp":1791557492742,"version":"4.3.4"},"reference-count":0,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T00:00:00Z","timestamp":1791504000000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Tilia mandshurica is an important woody nectar plant, but the genomic and transcriptional basis of its nectar sugar accumulation remains poorly understood. Here, we generated a chromosome-level reference genome for T. mandshurica and integrated comparative genomics, gene duplication analysis, RNA-seq across seven floral developmental stages, qRT-PCR validation, carbohydrate measurements and metabolite profiling. Gene family analysis revealed lineage-specific expansion of families involved in carbohydrate metabolism, ion transport and specialized metabolism. Ks and synteny analyses identified an ancient Eocene whole-genome duplication likely shared with Craigia yunnanensis, whereas duplication-mode analysis indicated that subsequent small-scale duplications contributed to lineage-specific duplicate retention. Among the enriched carbohydrate-related categories, trehalose-phosphatase activity provided a link between genome evolution and floral sugar accumulation. Sixteen trehalose-phosphate phosphatase (TPP) genes separated into fructose-positive C1 and fructose-negative C2 classes, with strong divergence at both the gene level (\u0394 = 1.060) and module level (\u0394 = 1.294). C1 TPP genes tracked fructose accumulation, whereas C2 genes followed starch-related developmental programs. Coexpression analysis further revealed contrasting network architectures: C1 TPP genes formed a convergent network with enriched vacuolar\/tonoplast-related targets, whereas C2 genes showed a dispersed architecture with no consensus targets. C1-co-expressed candidates included genes related to vacuolar ion homeostasis, cell-wall\/glycan remodeling, and isoprenoid\/carotenoid metabolism. Together, these results support a model in which duplicated TPP genes are associated with distinct carbohydrate-associated transcriptional programs for starch remobilization and fructose-rich nectar formation. This study provides a genomic resource for Tilia and identifies candidate TPP-centered networks for nectar sugar accumulation in woody honey plants.<\/jats:p>","DOI":"10.1093\/treephys\/tpag151","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T11:50:25Z","timestamp":1791373825000},"source":"Crossref","is-referenced-by-count":0,"title":["Chromosome-level genome assembly of\n                    <i>Tilia mandshurica<\/i>\n                    reveals divergence of duplicated\n                    <i>TPP<\/i>\n                    genes associated with fructose-rich nectar formation"],"prefix":"10.1093","author":[{"given":"Lin","family":"Lin","sequence":"first","affiliation":[{"name":"Forestry College, Beihua University , Jilin 132013 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayi","family":"Du","sequence":"additional","affiliation":[{"name":"Forestry College, Beihua University , Jilin 132013 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingshan","family":"Li","sequence":"additional","affiliation":[{"name":"Guangxi Key Laboratory of Agro-environment and Agro-products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University , Nanning 530004, Guangxi ,","place":["P.R. China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cong","family":"Yu","sequence":"additional","affiliation":[{"name":"Forestry College, Beihua University , Jilin 132013 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le","family":"Chen","sequence":"additional","affiliation":[{"name":"Forestry College, Beihua University , Jilin 132013 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenzheng","family":"Li","sequence":"additional","affiliation":[{"name":"Forestry College, Beihua University , Jilin 132013 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fucai","family":"Xia","sequence":"additional","affiliation":[{"name":"Forestry College, Beihua University , Jilin 132013 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0432-4251","authenticated-orcid":false,"given":"Huaizhi","family":"Mu","sequence":"additional","affiliation":[{"name":"Forestry College, Beihua University , Jilin 132013 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,9]]},"container-title":["Tree Physiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/treephys\/advance-article-pdf\/doi\/10.1093\/treephys\/tpag151\/71788150\/tpag151.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/treephys\/advance-article-pdf\/doi\/10.1093\/treephys\/tpag151\/71788150\/tpag151.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T14:21:43Z","timestamp":1791555703000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/treephys\/advance-article\/doi\/10.1093\/treephys\/tpag151\/8898640"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,9]]},"references-count":0,"URL":"https:\/\/doi.org\/10.1093\/treephys\/tpag151","relation":{},"ISSN":["1758-4469"],"issn-type":[{"value":"1758-4469","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,9]]},"article-number":"tpag151"}}