Most terrestrial plants use C3 photosynthesis to fix carbon. In multiple plant lineages a modified system known as C4 photosynthesis has evolved. To better understand the molecular patterns associated with induction of C4 photosynthesis, the genus Flaveria that contains C3 and C4 species was used. A base to tip maturation gradient of leaf anatomy was defined, and RNA sequencing was undertaken along this gradient for two C3 and two C4 Flaveria species. Key C4 traits including vein density, mesophyll and bundle sheath cross-sectional area, chloroplast ultrastructure, and abundance of transcripts encoding proteins of C4 photosynthesis were quantified. Candidate genes underlying each of these C4 characteristics were identified. Principal components analysis indicated that leaf maturation and the photosynthetic pathway were responsible for the greatest amount of variation in transcript abundance. Photosynthesis genes were over-represented for a prolonged period in the C4 species. Through comparison with publicly available data sets, we identify a small number of transcriptional regulators that have been up-regulated in diverse C4 species. The analysis identifies similar patterns of expression in independent C4 lineages and so indicates that the complex C4 pathway is associated with parallel as well as convergent evolution.

Sapotaceae belongs to the heterogeneous order Ericales and exhibits extensive diversity in floral morphology. Although pentamery is widespread and probably the ancestral condition, some clades are extremely variable in merism, with fluctuations between tetramery to hexamery and octomery, affecting different floral organs to different degrees. We assessed the different states of merism in Sapotaceae to determine the evolution of this character among different clades. The floral morphology and development of nine species from eight genera were investigated using scanning electron microscopy (SEM). Furthermore, floral characters related to merism were mapped onto a phylogenetic tree to analyse the distribution and evolutionary significance of merism in the family. Developmental evidence shows that changes in merism are linked to a concerted multiplication of organs among whorls and an increase in whorls through the displacement of organs. Although pentamery is reconstructed as the ancestral condition, a reduction to tetramery or an increase to a higher merism (mainly hexamery or octomery) has evolved at least five times in the family. Fluctuations in merism between different whorls are not random but occur in a coordinated pattern, presenting strong synapomorphies for selected clades. Octomery has evolved at least twice, in Isonandreae from tetramery and in Sapoteae-Mimusopinae from pentamery. Hexamery has evolved at least three times, independently in Northia, the Palaquium clade of Isonandreae and derived from octomery in Sapoteae-Mimusopinae. Three possibilities of merism increase have been identified in Sapotaceae: (1) a concerted increase affecting all organs more or less equally (Palaquium clade of Isonandreae, Sapoteae); (2) a coordinated increase in petals, stamens and mostly carpels without effect on sepals (Labourdonnaisia, Payena-Madhuca clade of Isonandreae); (3) an increase in carpels independently of other organs (Burckella, Letestua, Labramia, etc.). A major shift affecting all Sapotaceae, except Isonandreae, is the sterilization or loss of the antesepalous stamen whorl. The presence of two fertile stamen whorls in Isonandreae indicates a possible reversal or a retained plesiomorphy. In a number of genera, stamens are secondarily increased independently of changes in merism. Descriptions of flowers listing only organ numbers are thus misleading in the inference of evolutionary relationships, as they do not differentiate between changes in merism affecting the number of perianth whorls and other changes affecting the androecium, such as sterilization, loss or occasional doubling of antepetalous stamens.

The cultivation of many crops relies on the formation of chimeric plants, where roots from one variety are grafted onto the shoot of another. A new study uncovers how two plants connect and demonstrates that the root and shoot do not contribute equally to the union.

With at least 60 independent origins spanning monocotyledons and dicotyledons, the C4 photosynthetic pathway represents one of the most remarkable examples of convergent evolution. The recurrent evolution of this highly complex trait involving alterations to leaf anatomy, cell biology and biochemistry allows an increase in productivity by ~50% in tropical and subtropical areas. The extent to which separate lineages of C4 plants use the same genetic networks to maintain C4 photosynthesis is unknown. We developed a new informatics framework to enable deep evolutionary comparison of gene expression in species lacking reference genomes. We exploited this to compare gene expression in species representing two independent C4 lineages (Cleome gynandra and Zea mays) whose last common ancestor diverged ~140 million years ago. We define a cohort of 3,335 genes that represent conserved components of leaf and photosynthetic development in these species. Furthermore, we show that genes encoding proteins of the C4 cycle are recruited into networks defined by photosynthesis-related genes. Despite the wide evolutionary separation and independent origins of the C4 phenotype, we report that these species use homologous transcription factors to both induce C4 photosynthesis and to maintain the cell specific gene expression required for the pathway to operate. We define a core molecular signature associated with leaf and photosynthetic maturation that is likely shared by angiosperm species derived from the last common ancestor of the monocotyledons and dicotyledons. We show that deep evolutionary comparisons of gene expression can reveal novel insight into the molecular convergence of highly complex phenotypes and that parallel evolution of trans-factors underpins the repeated appearance of C4 photosynthesis. Thus, exploitation of extant natural variation associated with complex traits can be used to identify regulators. Moreover, the transcription factors that are shared by independent C4 lineages are key targets for engineering the C4 pathway into C3 crops such as rice. © 2014 Aubry et al.

C4 photosynthesis is a complex trait that has a high degree of natural variation, involving anatomical and biochemical changes relative to the ancestral C3 state. It has evolved at least 66 times across a variety of lineages and the evolutionary route from C3 to C4 is likely conserved but not necessarily genetically identical. As such, a variety of C4 species are needed to identify what is fundamental to the C4 evolutionary process in a global context. In order to identify the genetic components of C4 form and function, a number of species are used as genetic models. These include Zea mays (maize), Sorghum bicolor (sorghum), Setaria viridis (Setaria), Flaveria bidentis, and Cleome gynandra. Each of these species has different benefits and challenges associated with its use as a model organism. Here, we propose that RNA profiling of a large sampling of C4, C3-C4, and C3 species, from as many lineages as possible, will allow identification of candidate genes necessary and sufficient to confer C4 anatomy and/or biochemistry. Furthermore, C4 model species will play a critical role in the functional characterization of these candidate genes and identification of their regulatory elements, by providing a platform for transformation and through the use of gene expression profiles in mesophyll and bundle sheath cells and along the leaf developmental gradient. Efforts should be made to sequence the genomes of F. bidentis and C. gynandra and to develop congeneric C3 species as genetic models for comparative studies. In combination, such resources would facilitate discovery of common and unique C4 regulatory mechanisms across genera. © 2013 Springer Science+Business Media Dordrecht.