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annuum, three of which are located in the clusters, indicating that a portion of genes was pseudogenized after tandem duplications. Expression of two Class I genes was complementary to each other, and all the genes in Class II were not expressed in roots of C. annuum. Two Class II genes (CA00g90790 and CA05g1706 showed upregulated expression as the chili pepper leaves matured, and two Class II genes (CA05g17060 and CA12g2007 showed downregulated expression with the maturation of fruits, consistent with flavonoid accumulation trends
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