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Kuntze (Brazilian pine) is a native conifer of high ecological and socioeconomic value and serves as a model for studying zygotic and somatic embryogenesis (SE). Here, we combined biomass composition and targeted metabolomics to compare embryo development in seeds and embryogenic cultures, to identify metabolic features associated with embryogenic competence. We analyzed zygotic embryos at globular, cotyledonal and mature stages, their corresponding megagametophytes and two somatic embryogenic cell lines (Responsive and Blocked) with different embryogenic potential at proliferation and maturation phases. A total of 116 metabolites and biomass components belonging to six major classes (amino acids and their derivatives, fatty acids, sugars and starch, sugar alcohols, phosphorylated compounds and organic acids) were identified. Biomass data showed a marked shift from a globular embryo dominated by insoluble residue to starch- and protein-rich late zygotic stages, whereas somatic lines retained high proportions of insoluble residue and showed limited reserve accumulation. Hierarchical clustering and multivariate discriminant analysis revealed distinct metabolic signatures for zygotic and somatic systems, with amino acids and organic acids emerging as key discriminants. Isocitrate showed the highest variable importance in projection score and was positively correlated with several amino acids and soluble sugars. Co-metabolic network analysis further indicated that amino acid and organic acid classes underwent the strongest topological reorganization, forming increasingly modular and connected networks in zygotic embryos compared with somatic cultures. Together, these results highlight central carbon and nitrogen metabolism as key axes distinguishing zygotic and SE in A. angustifolia, and identify specific metabolites and network features as candidate markers of embryogenic competence.<\/jats:p>","DOI":"10.1093\/treephys\/tpag094","type":"journal-article","created":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T17:35:34Z","timestamp":1783359334000},"source":"Crossref","is-referenced-by-count":0,"title":["Metabolome signatures during zygotic and somatic embryogenesis of\n                    <i>Araucaria angustifolia<\/i>"],"prefix":"10.1093","volume":"46","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9289-4328","authenticated-orcid":false,"given":"Bruno Viana","family":"Navarro","sequence":"first","affiliation":[{"name":"Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of S\u00e3o Paulo , Rua do Mat\u00e3o 277, Cidade Universit\u00e1ria, S\u00e3o Paulo, SP 05508-090 ,","place":["Brazil"]},{"name":"Laboratory of Plant Physiological Ecology, Department of Botany, Institute of Biosciences, University of S\u00e3o Paulo , Rua do Mat\u00e3o 277, Cidade Universit\u00e1ria, S\u00e3o Paulo, SP 05508-090 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7721-9260","authenticated-orcid":false,"given":"Jean-Christophe","family":"Cocuron","sequence":"additional","affiliation":[{"name":"BioAnalytical Facility, University of North Texas , 1155 Union Circle #310979, Denton, TX 76203, \u00a0","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5318-2771","authenticated-orcid":false,"given":"Leandro Francisco","family":"de Oliveira","sequence":"additional","affiliation":[{"name":"Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of S\u00e3o Paulo , Rua do Mat\u00e3o 277, Cidade Universit\u00e1ria, S\u00e3o Paulo, SP 05508-090 ,","place":["Brazil"]},{"name":"Lignin Lab, Department of Botany, Institute of Biosciences, University of S\u00e3o Paulo , Rua do Mat\u00e3o 277, Cidade Universit\u00e1ria, S\u00e3o Paulo, SP 05508-090 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9412-0545","authenticated-orcid":false,"given":"Marina Camara Mattos","family":"Martins","sequence":"additional","affiliation":[{"name":"Laboratory of Plant Physiological Ecology, Department of Botany, Institute of Biosciences, University of S\u00e3o Paulo , Rua do Mat\u00e3o 277, Cidade Universit\u00e1ria, S\u00e3o Paulo, SP 05508-090 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5816-5340","authenticated-orcid":false,"given":"Vin\u00edcius","family":"Jardim","sequence":"additional","affiliation":[{"name":"Laboratory of Plant Physiological Ecology, Department of Botany, Institute of Biosciences, University of S\u00e3o Paulo , Rua do Mat\u00e3o 277, Cidade Universit\u00e1ria, S\u00e3o Paulo, SP 05508-090 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4696-1811","authenticated-orcid":false,"given":"Ana Paula","family":"Alonso","sequence":"additional","affiliation":[{"name":"BioAnalytical Facility, University of North Texas , 1155 Union Circle #310979, Denton, TX 76203, \u00a0","place":["United States"]},{"name":"BioDiscovery Institute and Department of Biological Sciences, University of North Texas , 1155 Union Circle #305220, Denton, TX 76203-5017, \u00a0","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5455-8136","authenticated-orcid":false,"given":"Marcos S","family":"Buckeridge","sequence":"additional","affiliation":[{"name":"Laboratory of Plant Physiological Ecology, Department of 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