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While their physiological and biochemical properties are well studied, the regulatory mechanisms controlling juice sac initiation remain poorly understood. In this study, we compared two cultivars of citron (\n                      <jats:italic>Citrus medica<\/jats:italic>\n                      L.)\u2014the\n                      <jats:italic>Calabria<\/jats:italic>\n                      citron, which develops juice sacs normally, and the\n                      <jats:italic>Yemenite<\/jats:italic>\n                      citron, which does not\u2014across four developmental stages: closed flowers, flowers at anthesis, and fruitlets at one and two weeks post-anthesis. We performed a comparative transcriptomic analysis of endocarp cells, followed by Weighted Gene Co-Expression Network Analysis (WGCNA) and a metabolomic analysis of whole ovaries and fruitlets. As expected, the\n                      <jats:italic>Calabria<\/jats:italic>\n                      endocarp exhibited higher expression of genes associated with cell wall formation, DNA replication, and cell proliferation, particularly two weeks post-anthesis. In contrast, stress-related genes were more abundant in the\n                      <jats:italic>Yemenite<\/jats:italic>\n                      endocarp.\n                      <jats:italic>Calabria<\/jats:italic>\n                      ovaries and fruitlets showed an increase in amino acids, whereas those of the\n                      <jats:italic>Yemenite<\/jats:italic>\n                      citron exhibited induction of TCA cycle and energy metabolism pathways. Integrating transcriptomic and metabolomic data revealed significant enrichment of carbohydrate and energy metabolism pathways in the\n                      <jats:italic>Yemenite<\/jats:italic>\n                      citron. Additionally, we identified a transcription factor regulatory network that may contribute to juice sac initiation. These findings provide new insights into the molecular processes underlying juice sac initiation and establish a foundation for future research aimed at elucidating its regulatory mechanisms.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s00425-026-05008-9","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T15:46:00Z","timestamp":1777995960000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptomic and metabolomic changes associated with the induction and initiation of juice sacs in citrus fruit"],"prefix":"10.1007","volume":"263","author":[{"given":"Siwar","family":"Assili","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dor","family":"Haim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adi","family":"Doron-Faigenboim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ido","family":"Nir","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7755-2124","authenticated-orcid":false,"given":"Avi","family":"Sadka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,5,5]]},"reference":[{"key":"5008_CR1","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1146\/ANNUREV-ARPLANT-083023-034055\/CITE\/REFWORKS","volume":"76","author":"CT Anderson","year":"2025","unstructured":"Anderson CT, Pelloux J (2025) The dynamics, degradation, and afterlives of pectins: influences on cell wall assembly and structure, plant development and physiology, agronomy, and biotechnology. 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