Evolutionary genomics of C4 photosynthesis in grasses requires a large species sampling

Gains and losses of metabolic function inferred from a phylotranscriptomic analysis of algae

Hidden Markov models representing 167 protein sequence families were used to infer the presence or absence of homologs within the transcriptomes of 183 algal species/strains. Statistical analyses of the distribution of HMM hits across major clades of algae, or at branch points on the phylogenetic tree of 98 chlorophytes, confirmed and extended known cases of metabolic loss and gain, most notably the loss of the mevalonate pathway for terpenoid synthesis in green algae but not, as we show here, in the streptophyte algae. Evidence for novel events was found as well, most remarkably in the recurrent and coordinated gain or loss of enzymes for the glyoxylate shunt. We find, as well, a curious pattern of retention (or re-gain) of HMG-CoA synthase in chlorophytes that have otherwise lost the mevalonate pathway, suggesting a novel, co-opted function for this enzyme in select lineages. Finally, we find striking, phylogenetically linked distributions of coding sequences for three pathways that synthesize the major membrane lipid phosphatidylcholine, and a complementary phylogenetic distribution pattern for the non-phospholipid DGTS (diacyl-glyceryl-trimethylhomoserine). Mass spectrometric analysis of lipids from 25 species was used to validate the inference of DGTS synthesis from sequence data.

The recurrent assembly of C4 photosynthesis, an evolutionary tale

Today, plants using C4 photosynthesis are widespread and important components of major tropical and subtropical biomes, but the events that led to their evolution and success started billions of years ago (bya). A CO2-fixing enzyme evolved in the early Earth atmosphere with a tendency to confuse CO2 and O2 molecules. The descendants of early photosynthetic organisms coped with this property in the geological eras that followed through successive fixes, the latest of which is the addition of complex CO2-concentrating mechanisms such as C4 photosynthesis. This trait was assembled from bricks available in C3 ancestors, which were altered to fulfill their new role in C4 photosynthesis. The existence of C4-suitable bricks probably determined the lineages of plants that could make the transition to C4 photosynthesis, highlighting the power of contingency in evolution. Based on the latest findings in C4 research, we present the evolutionary tale of C4 photosynthesis, with a focus on the general evolutionary phenomena that it so wonderfully exemplifies.

C₄ photosynthesis: from evolutionary analyses to strategies for synthetic reconstruction of the trait

C₄ photosynthesis represents the most productive modes of photosynthesis in land plants and some of the most productive crops on the planet, such as maize and sugarcane, and many ecologically important native plants use this type of photosynthesis. Despite its ecological and economic importance, the genetic basis of C₄ photosynthesis remains largely unknown. Even many fundamental aspects of C₄ biochemistry, such as the molecular identity of solute transporters, and many aspects of C₄ plant leaf development, such as the Kranz anatomy, are currently not understood. Here, we review recent progress in gaining a mechanistic understanding of the complex C₄ trait through comparative evolutionary analyses of C₃ and C₄ species.

Phylogeny-based comparative methods question the adaptive nature of sporophytic specializations in mosses

Adaptive evolution has often been proposed to explain correlations between habitats and certain phenotypes. In mosses, a high frequency of species with specialized sporophytic traits in exposed or epiphytic habitats was, already 100 years ago, suggested as due to adaptation. We tested this hypothesis by contrasting phylogenetic and morphological data from two moss families, Neckeraceae and Lembophyllaceae, both of which show parallel shifts to a specialized morphology and to exposed epiphytic or epilithic habitats. Phylogeny-based tests for correlated evolution revealed that evolution of four sporophytic traits is correlated with a habitat shift. For three of them, evolutionary rates of dual character-state changes suggest that habitat shifts appear prior to changes in morphology. This suggests that they could have evolved as adaptations to new habitats. Regarding the fourth correlated trait the specialized morphology had already evolved before the habitat shift. In addition, several other specialized "epiphytic" traits show no correlation with a habitat shift. Besides adaptive diversification, other processes thus also affect the match between phenotype and environment. Several potential factors such as complex genetic and developmental pathways yielding the same phenotypes, differences in strength of selection, or constraints in phenotypic evolution may lead to an inability of phylogeny-based comparative methods to detect potential adaptations.