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Many cellular reactions occur in linear metabolic pathways where gene products act sequentially to produce needed compounds. The interrelationships between the products of these loci raises the question of whether they evolve in concert or independently. Previous research addressing this question indicated that in the anthocyanin pathway, which produces important secondary metabolites in plants, the genes encoding downstream enzymes show an accelerated rate of evolution when compared to upstream loci. The hypothesized cause of these differences has been attributed to relaxed selective constraint. This pattern and process has not, however, been tested in other systems. The carotenoid biosynthetic pathway, which also produces important colored secondary metabolites in plants, presents an appropriate system for an additional test. To produce a dataset suitable for this test, known mRNA sequences from four carotenoid biosynthetic enzymes of Solanum lycopersicum (tomato) were used to identify homologous sequences in taxa representing a broad range of angiosperms. Comparisons between Phytoene desaturase, Zeta-carotene desaturase, Lycopene beta-cyclase and Zeaxanthin epoxidase show that the downstream enzymes in the pathway have greater nucleotide diversity, nonsynonymous substitution rates and synonymous substitution rates. Evidence for selective constraint and an increase in the proportion of nucleotide sites under selective constraint has also been observed.

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