Molecular evolution of the exon 2 of CHS genes and the possibility of its application to plant phylogenetic analysis

The exon 2 of chalcone synthase (CHS) gene is relatively conserved during e volution. In this study, three exon 2 fragments from two species in gymnosp erm (Cycas panzhihuaensis, Ginkgo biloba) and seven from four species in an giosperm ((Magnolia denudata, Salix babylonica, Nymphaea tetragona, Camelli a japonica) have been amplified by PCR from genomic DNA and sequenced. Toge ther with other 73 sequences of CHS collected from EMBL database and litera ture, these sequences, which embrace 19 families of gymnosperm and angiospe rm, have been analyzed for their phylogenetic relations by parsimony method . The result indicated that sequences from the same systematic family usual ly grouped together except those from Theaceae, Magnoliaceae and Nymphaeace ae. The relative rate test revealed the rate heterogeneity of CHS genes amo ng the families. For the nucleotide substitution the sequences from Asterac eae and Solanaceae evolve faster than those from the other families analyze d while the sequences from Poaceae, Asteraceae and Solanaceae evolve faster for the nonsynonymous substitution. These results suggest that the duplica tion and extinction events of CHS genes are different among systematic fami lies, therefore it seems impractical to look for orthologous sequences from CHS genes to study plant phylogeny at the family level and/or above. Howev er, it is possible to do so below the family level.