Transcriptome analysis of color-related gene expression in three differently colored cherry tomato fruits

Tomato (Lycopersicon esculentum Mill.) is a globally important fruit. However, the gene expression in differently colored cherry tomato fruits is not well understood. In this study, three typical cherry tomato fruit colors (yellow, green, and red) were selected to explore genes related to color transformation through transcriptome analysis. The results showed that the soluble solid content was highest in the yellow fruits (5.5%), followed by the green and red fruits at 4.9 and 4.5%, respectively. A total of 1547 genes were upregulated and 2752 genes were downregulated in the yellow fruits compared with the green fruits; further, 913 genes were upregulated and 1863 genes were downregulated in the yellow fruits compared with the red fruits. The most upregulated pathways obtained through Kyoto Encyclopedia of Genes and Genomes analysis included photosynthesis, glutathione metabolism, and flavonoid biosynthesis in the yellow fruits compared with the red fruits. Our observations suggest that the three cherry tomato fruits utilize different pathways in color determination. The genes LOC101257857 and LOC101253805 were upregulated in the yellow fruits, while LOC101246495, LOC101248036, and LOC101260960 were upregulated in the green fruits. This work contributes to the understanding of the gene expression and pathways in fruit color change, providing new insights into improving the quality of cherry tomato fruits.