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Background  Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses the key reaction in the photosynthetic assimilation of CO 2 . In C 4  plants CO 2  is supplied to Rubisco by an auxiliary CO 2 -concentrating pathway that helps to maximize the carboxylase activity of the enzyme while suppressing its oxygenase activity. As a consequence, C 4  Rubisco exhibits a higher maximum velocity but lower substrate specificity compared with the C 3  enzyme. Specific amino-acids in Rubisco are associated with C 4  photosynthesis in monocots, but it is not known whether selection has acted on Rubisco in a similar way in eudicots.    Methodology/Principal Findings  We investigated Rubisco evolution in Amaranthaceae  sensu lato  (including Chenopodiaceae), the third-largest family of C 4  plants, using phylogeny-based maximum likelihood and Bayesian methods to detect Darwinian selection on the chloroplast  rbcL  gene in a sample of 179 species. Two Rubisco residues, 281 and 309, were found to be under positive selection in C 4  Amaranthaceae with multiple parallel replacements of alanine by serine at position 281 and methionine by isoleucine at position 309. Remarkably, both amino-acids have been detected in other C 4  plant groups, such as C 4  monocots, illustrating a striking parallelism in molecular evolution.    Conclusions/Significance  Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco.

Rubisco Evolution in C4 Eudicots: An Analysis of Amaranthaceae Sensu Lato