| Summary: | Isomerization of 9,15,9′-tri-<i>cis</i>-ζ-carotene mediated by 15-<i>cis</i>-ζ-carotene isomerase Z-ISO is a critical step in the biosynthesis of carotenoids, which define fruit color. The tomato clade (<i>Solanum</i> section Lycopersicon) comprises the cultivated tomato (<i>Solanum lycopersicum</i>) and 12 related wild species differing in fruit color and, thus, represents a good model for studying carotenogenesis in fleshy fruit. In this study, we identified homologous <i>Z-ISO</i> genes, including 5′-UTRs and promoter regions, in 12 <i>S. lycopersicum</i> cultivars and 5 wild tomato species (red-fruited <i>Solanum pimpinellifolium</i>, yellow-fruited <i>Solanum cheesmaniae</i>, and green-fruited <i>Solanum chilense</i>, <i>Solanum habrochaites</i>, and <i>Solanum pennellii</i>). <i>Z-ISO</i> homologs had a highly conserved structure, suggesting that Z-ISO performs a similar function in tomato species despite the difference in their fruit color. <i>Z-ISO</i> transcription levels positively correlated with the carotenoid content in ripe fruit of the tomatoes. An analysis of the <i>Z-ISO</i> promoter and 5′-UTR sequences revealed over 130 <i>cis</i>-regulatory elements involved in response to light, stresses, and hormones, and in the binding of transcription factors. Green- and red/yellow-fruited <i>Solanum</i> species differed in the number and position of <i>cis</i>-elements, indicating changes in the transcriptional regulation of <i>Z-ISO</i> expression during tomato evolution, which likely contribute to the difference in fruit color.
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