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The exon 2 of chalcone synthase (CHS) gene is relatively conserved during evolution.In this study,three exon 2 fragments from two species in gymnosperm (Cycas panzhihuaensis,Ginkgo biloba) and seven from four species in angiosperm (Magnolia denudata,Salix babylonica,Nymphaea tetragona,Camellia japonica) have been amplified by PCR from genomic DNA and sequenced.Together with other 73 sequences of CHS collected from EMBL database and literature,these sequences,which embrace 19 families of gymnosperm and angiosperm,have been analyzed for their phylogenetic relations by parsimony method.The result indicated that sequences from the same systematic family usually grouped together except those from Theaceae,Magnoliaceae and Nymphaeaceae.The relative rate test revealed the rate heterogeneity of CHS genes among the families.For the nucleotide substitution the sequences from Asteraceae and Solanaceae evolve faster than those from the other families analyzed while the sequences from Poaceae,Asteraceae and Solanaceae evolve faster for the nonsynonymous substitution.These results suggest that the duplication and extinction events of CHS genes are different among systematic families,therefore it seems impractical to look for orthologous sequences from CHS genes to study plant phylogeny at the family level and/or above.However,it is possible to do so below the family level.