Chalcone synthase (CHS, EC 188.8.131.52) is a key enzyme in the biosynthesis of flavonoids, which plays an important role in flower pigmentation and protection against UV, plant-microbe interactions, and plant fertility. In many plants, genes encoding CHS constitute a multigene family, wherein sequence and functional divergence occurred repeatedly. Since the genome of rice (Oryza sativa) has been completely sequenced, many genes possessing typical CHS domains were assumed to be chs genes, although the sequence and functional divergence of this large gene family has not as yet been investigated. In this study, all putative CHS members from O. sativa were analyzed by the phylogenetic methods. Our results indicate that the members of rice CHS superfamily probably diverged into four branches. Members of each branch may perform specific functions. Two conserved chs genes clustered with chs genes from other monocotyledon and dicotyledon species are believed to encode true CHSs responsible for the biosynthesis of flavonoids and anthocyanins. Two chs genes in one distant branch might play some functions in fertility. Several other putative chs genes were clustered together, and the function of this branch could not be predicted. Many tentative chs genes were clustered together with fatty acid synthase (FAS) genes. These genes may belong to the fas gene family.
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