Expression data from tomato fruit at three ripening stages (MG, Br, B10) in wild type lines (Alsa Craig, AC, and M82) and five tomato carotenoid mutants: apricot (at), yellow flesh (r), tangerine (t), Beta (B), and Delta (Del).

The integrated analysis highlighted regulatory links between transcripts and metabolites and pointed to lycopene cyclization as a central node in isoprenoid network rewiring during ripening, improving our understanding of mechanisms controlling isoprenoid accumulation in tomato fruit. Carotenoids are key bioactive compounds, and tomato is a major model to study how genetic variation shapes their accumulation during fruit ripening.

We profiled five tomato carotenoid mutants (apricot at, yellow flesh r, tangerine t, Delta Del, Beta B) across three ripening stages using Affymetrix gene-expression arrays integrated with targeted isoprenoid metabolomics (carotenoids, chlorophylls, tocochromanols, quinones, ABA) and correlation analyses. The data reveal strong stage-dependent remodeling and highlight lycopene cyclization as a central hub in isoprenoid pathway rewiring during ripening.