S (residues 281 and 309) were shown to be under positive Daclatasvir (dihydrochloride) site selection within C4 clades while under relaxed or purifying selection within C3 clades with a posterior probability .0.99 by BEB in the A model for C4 branches. Both sites had only two alternative amino acids in this dataset (Table 2). One of the two alternative amino acids was more frequent among C4 species, while the other was more frequent among C3 species (Table 2), but there were no fixed differences between C4 and C3 species. We refer to amino acids more frequently associated with C4 taxa as the `C4′ amino acids, but only for the sake of brevity, as they are not invariantly associated with C4 photosynthesis. Pagel’s test of correlated character evolution [40] on phylogeny showed significant positive associations (p-value ,0.05) between the presence of C4 photosynthesis and the presence of `C4′ amino acids at sites 281 and 309, shown to be under positive selection along C4 branches.Analysis of correlated evolution on phylogeniesClosely related taxa are not independent data points and they consequently violate the assumptions of conventional statistical methods [39]. Thus, we used analysis of correlated evolution on phylogenies to test the significance of correlation between pairs of discrete characters: (1) the presence/absence of C4 photosynthesis and (2) the presence/absence of particular amino-acid at sites found to be under positive selection along C4 branches in the A model of codeml. For this purpose, we used the phylogeny obtained using RAxML (see above) and performed Pagel’s test of correlated (discrete) character evolution [40] implemented in the Mesquite package (version 2.72) [41]. Test was performed separately for each Rubisco residue under positive selection along C4 branches and Bonferroni correction was performed for simultaneous statistical testing.Structural analysis of RubiscoWe used the published Rubisco protein structure from spinach (Spinacia oleracea, Amaranthaceae) from data file 1RBO [42] obtained from the RCSB Protein Data Bank. Throughout the paper, the numbering of Rubisco large subunit residues is based on the spinach sequence. The Crenolanib locations and properties of individual amino acids in the Rubisco structure were analysed using DeepView ?Swiss-PdbViewer 24195657 v.3.7 [43] and by CUPSAT [44].Discussion Widespread positive selection on RubiscoAs the performance of Rubisco can directly affect plant growth and crop yields, substantial efforts have been made to study its structure and function, with the ultimate aim of trying to improve Rubisco performance [50]. The last few years have brought new approaches to improving our understanding of Rubisco evolution and its genetic mechanisms. The initial molecular-phylogenetic analysis of rbcL showed that positive selection is widespread among all main lineages of land plants, but is restricted to a relatively small number of Rubisco amino acid residues within functionally important sites [6]. Following studies showed that rbcL is under positive selection in particular taxonomic groups [26,27,51,52,53,54,55,56]. Coevolution of residues is common in Rubisco of land plants as well as positive selection and there is an overlap between coevolving and positively selected residues [57]. Hence, phylogeny-based genetic analyses suggest there has been a constant fine-tuning of Rubisco to optimize its performance in specific conditions, in agreement with empirical observations that Rubisco enzymes from different organisms show d.S (residues 281 and 309) were shown to be under positive selection within C4 clades while under relaxed or purifying selection within C3 clades with a posterior probability .0.99 by BEB in the A model for C4 branches. Both sites had only two alternative amino acids in this dataset (Table 2). One of the two alternative amino acids was more frequent among C4 species, while the other was more frequent among C3 species (Table 2), but there were no fixed differences between C4 and C3 species. We refer to amino acids more frequently associated with C4 taxa as the `C4′ amino acids, but only for the sake of brevity, as they are not invariantly associated with C4 photosynthesis. Pagel’s test of correlated character evolution [40] on phylogeny showed significant positive associations (p-value ,0.05) between the presence of C4 photosynthesis and the presence of `C4′ amino acids at sites 281 and 309, shown to be under positive selection along C4 branches.Analysis of correlated evolution on phylogeniesClosely related taxa are not independent data points and they consequently violate the assumptions of conventional statistical methods [39]. Thus, we used analysis of correlated evolution on phylogenies to test the significance of correlation between pairs of discrete characters: (1) the presence/absence of C4 photosynthesis and (2) the presence/absence of particular amino-acid at sites found to be under positive selection along C4 branches in the A model of codeml. For this purpose, we used the phylogeny obtained using RAxML (see above) and performed Pagel’s test of correlated (discrete) character evolution [40] implemented in the Mesquite package (version 2.72) [41]. Test was performed separately for each Rubisco residue under positive selection along C4 branches and Bonferroni correction was performed for simultaneous statistical testing.Structural analysis of RubiscoWe used the published Rubisco protein structure from spinach (Spinacia oleracea, Amaranthaceae) from data file 1RBO [42] obtained from the RCSB Protein Data Bank. Throughout the paper, the numbering of Rubisco large subunit residues is based on the spinach sequence. The locations and properties of individual amino acids in the Rubisco structure were analysed using DeepView ?Swiss-PdbViewer 24195657 v.3.7 [43] and by CUPSAT [44].Discussion Widespread positive selection on RubiscoAs the performance of Rubisco can directly affect plant growth and crop yields, substantial efforts have been made to study its structure and function, with the ultimate aim of trying to improve Rubisco performance [50]. The last few years have brought new approaches to improving our understanding of Rubisco evolution and its genetic mechanisms. The initial molecular-phylogenetic analysis of rbcL showed that positive selection is widespread among all main lineages of land plants, but is restricted to a relatively small number of Rubisco amino acid residues within functionally important sites [6]. Following studies showed that rbcL is under positive selection in particular taxonomic groups [26,27,51,52,53,54,55,56]. Coevolution of residues is common in Rubisco of land plants as well as positive selection and there is an overlap between coevolving and positively selected residues [57]. Hence, phylogeny-based genetic analyses suggest there has been a constant fine-tuning of Rubisco to optimize its performance in specific conditions, in agreement with empirical observations that Rubisco enzymes from different organisms show d.
