One thousand plant transcriptomes and the phylogenomics of green plants

Abstract: Green plants (Viridiplantae) include around 450,000–500,000 species1, 2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life

Overview of recent Alcator C-Mod research

Research on the Alcator C-Mod tokamak [1] is focused on high particle- and power-density plasma regimes to understand particle and energy transport in the core, the dynamics of the H-mode pedestal, and scrape-off layer and divertor physics. The auxiliary heating is provided exclusively by RF waves, and both the physics and technology of RF heating and current drive are studied. The momentum which is manifested in strong toroidal rotation, in the absence of direct momentum input, has been shown to be transported in from the edge of the plasma following the L-H transition, with timescale comparable to that for energy transport. In discharges which develop internal transport barriers, the rotation slows first inside the barrier region, and then subsequently outside of the barrier foot. Heat pulse propagation studies using sawteeth indicate a very narrow region of strongly reduced energy transport, located near r/a = 0.5. Addition of on-axis ICRF heating arrests the buildup of density and impurities, leading to quasi-steady conditions. The quasi-coherent mode associated with enhanced D-Alpha (EDA) H-mode appears to be due to a resistive ballooning instability. As the pedestal pressure gradient and temperature are increased in EDA H-mode, small ELMs appear; detailed modelling indicates that these are due to intermediate n peeling-ballooning modes. Phase contrast imaging has been used to directly detect density fluctuations driven by ICRF waves in the core of the plasma, and mode conversion to an intermediate wavelength ion cyclotron wave has been observed for the first time. The bursty turbulent density fluctuations, observed to drive rapid cross-field particle transport in the edge plasma, appear to play a key role in the dynamics of the density limit. Preparations for quasi-steady-state advanced tokamak studies with lower hybrid current drive are well underway, and time dependent modelling indicates that regimes with high bootstrap fraction can be produced