Positive selection of Kranz and non-Kranz C(4) phosphoenolpyruvate carboxylase amino acids in Suaedoideae (Chenopodiaceae)

In subfamily Suaedoideae, four independent gains of C(4) photosynthesis are proposed, which includes two parallel origins of Kranz anatomy (sections Salsina and Schoberia) and two independent origins of single-cell C(4) anatomy (Bienertia and Suaeda aralocaspica). Additional phylogenetic support for this hypothesis was generated from sequence data of the C-terminal portion of the phosphoenolpyruvate carboxylase (PEPC) gene used in C(4) photosynthesis (ppc-1) in combination with previous sequence data. ppc-1 sequence was generated for 20 species in Suaedoideae and two outgroup Salsola species that included all types of C(4) anatomies as well as two types of C(3) anatomies. A branch-site test for positively selected codons was performed using the software package PAML. From labelling of the four branches where C(4) is hypothesized to have developed (foreground branches), residue 733 (maize numbering) was identified to be under positive selection with a posterior probability >0.99 and residue 868 at the >0.95 interval using Bayes empirical Bayes (BEB). When labelling all the branches within C(4) clades, the branch-site test identified 13 codons to be under selection with a posterior probability >0.95 by BEB; this is discussed considering current information on functional residues. The signature C(4) substitution of an alanine for a serine at position 780 in the C-terminal end (which is considered a major determinant of affinity for PEP) was only found in four of the C(4) species sampled, while eight of the C(4) species and all the C(3) species have an alanine residue; indicating that this substitution is not a requirement for C(4) function.