Rally important C4 monocots in the Poaceae, while C4 eudicots have been studied less intensively. The family Amaranthaceae sensu lato (i.e. including Chenopodiaceae) [17,18] contains about 180 genera and 2500 species, of which approximately 750 are C4 species [16], making it by far the 1379592 largest C4 family among eudicots and the third-largest among angiosperms (after Poaceae and Cyperaceae). C4 photosynthesis evolved at least 15 times within Amaranthaceae [16] making this family a good model to study coevolution of C4 photosynthesis and Rubisco. Notably, the Amaranthaceae exceed the Poaceae and Cyperaceae in the diversity of photosynthetic organ anatomy [19], and is the only angiosperm family containing terrestrial C4 plants that lack Kranz anatomy, with three species having a single-cell rather than the more usual dual-cell C4 system [20,21]. The predominantly tropical Amaranthaceae sensu stricto and primarily temperate and subtropical Chenopodiaceae have long been treated as two closely related families (see review in [19]) until the formal proposal that Chenopodiaceae should be included within the expanded Amaranthaceae based on a lack of separation between the two families in sequence data [17]. Amaranthaceae sensu lato (henceforth referred to as Amaranthaceae) constitutes the most diverse lineage of the Caryophyllales. Both C3 and C4 species from this family are adapted to a range of conditions from temperate meadows to the tropics, hot deserts and salt marshes. However, it has been shown that the abundance of C4 Amaranthaceae is correlated with precipitation but not temperature, in contrast to the abundance of C4 Poaceae and Cyperaceae, which is correlated with temperature but not precipitation [22]. Despite C4 Amaranthaceae showing different suites of anatomical and biochemical adaptations as well as ecological preferences compared to C4 Poaceae and Cyperaceae, like C4 monocots they possess faster but less CO2-specific Rubiscos than their C3 relatives [3,5,23]. Thus, Rubisco of C4 eudicots and monocots represents a notable example of convergent evolution of enzyme properties in phylogenetically distant groups. However, it is not known whether this functional GFT505 convergence in Rubisco kinetics evolved via similar or different structural changes in protein [24]. Molecular adaptation can be inferred from comparison of the rates of nonsynonymous (changing amino-acid protein sequence, dN) and synonymous (resulting in no change at the protein level, dS) mutations along a phylogenetic tree using maximum likelihoodand Bayesian frameworks [25]. Recently, such methodology has been applied to the chloroplast gene rbcL, which encodes the large subunit of Rubisco that forms the enzyme’s active site, and showed that positive Darwinian selection is acting within most lineages of plants [6]. Only a small fraction of Rubisco residues appear to be under positive selection, while most residues have been under buy Eltrombopag diethanolamine salt purifying selection [6]. Some of these residues have been shown to be under positive selection within C4 lineages of Poaceae and Cyperaceae 11967625 [26] and in the small Asteraceae genus, Flaveria [27], which contains both C3 and C4 species. However, no specific analysis has yet been made of Rubisco sequence evolution in a large group of C4 eudicots. In this study, we investigate positive selection on the rbcL gene of plants from the Amaranthaceae family and, in particular, focus on coevolution of Rubisco and C4 photosynthesis asking whether positive select.Rally important C4 monocots in the Poaceae, while C4 eudicots have been studied less intensively. The family Amaranthaceae sensu lato (i.e. including Chenopodiaceae) [17,18] contains about 180 genera and 2500 species, of which approximately 750 are C4 species [16], making it by far the 1379592 largest C4 family among eudicots and the third-largest among angiosperms (after Poaceae and Cyperaceae). C4 photosynthesis evolved at least 15 times within Amaranthaceae [16] making this family a good model to study coevolution of C4 photosynthesis and Rubisco. Notably, the Amaranthaceae exceed the Poaceae and Cyperaceae in the diversity of photosynthetic organ anatomy [19], and is the only angiosperm family containing terrestrial C4 plants that lack Kranz anatomy, with three species having a single-cell rather than the more usual dual-cell C4 system [20,21]. The predominantly tropical Amaranthaceae sensu stricto and primarily temperate and subtropical Chenopodiaceae have long been treated as two closely related families (see review in [19]) until the formal proposal that Chenopodiaceae should be included within the expanded Amaranthaceae based on a lack of separation between the two families in sequence data [17]. Amaranthaceae sensu lato (henceforth referred to as Amaranthaceae) constitutes the most diverse lineage of the Caryophyllales. Both C3 and C4 species from this family are adapted to a range of conditions from temperate meadows to the tropics, hot deserts and salt marshes. However, it has been shown that the abundance of C4 Amaranthaceae is correlated with precipitation but not temperature, in contrast to the abundance of C4 Poaceae and Cyperaceae, which is correlated with temperature but not precipitation [22]. Despite C4 Amaranthaceae showing different suites of anatomical and biochemical adaptations as well as ecological preferences compared to C4 Poaceae and Cyperaceae, like C4 monocots they possess faster but less CO2-specific Rubiscos than their C3 relatives [3,5,23]. Thus, Rubisco of C4 eudicots and monocots represents a notable example of convergent evolution of enzyme properties in phylogenetically distant groups. However, it is not known whether this functional convergence in Rubisco kinetics evolved via similar or different structural changes in protein [24]. Molecular adaptation can be inferred from comparison of the rates of nonsynonymous (changing amino-acid protein sequence, dN) and synonymous (resulting in no change at the protein level, dS) mutations along a phylogenetic tree using maximum likelihoodand Bayesian frameworks [25]. Recently, such methodology has been applied to the chloroplast gene rbcL, which encodes the large subunit of Rubisco that forms the enzyme’s active site, and showed that positive Darwinian selection is acting within most lineages of plants [6]. Only a small fraction of Rubisco residues appear to be under positive selection, while most residues have been under purifying selection [6]. Some of these residues have been shown to be under positive selection within C4 lineages of Poaceae and Cyperaceae 11967625 [26] and in the small Asteraceae genus, Flaveria [27], which contains both C3 and C4 species. However, no specific analysis has yet been made of Rubisco sequence evolution in a large group of C4 eudicots. In this study, we investigate positive selection on the rbcL gene of plants from the Amaranthaceae family and, in particular, focus on coevolution of Rubisco and C4 photosynthesis asking whether positive select.
