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Additional file 1: Supplementary Methods. Methodological detail on patient stool sample collection and proteomic analysis.

Precision medicine initiatives are being launched worldwide, each with the capacity to sequence many thousands to millions of human genomes. At the strategic planning level, all are debating the extent to which these resources will be directed towards rare diseases (and cancers) versus common diseases. However, these are not mutually exclusive choices. The organizational and governmental infrastructure created for rare diseases is extensible to common diseases. As we will explain, the underlying technology can also be used to identify drug targets for common diseases with a strategy focused on naturally occurring human knockouts. This flips on its head the prevailing modus operandi of studying people with diseases of interest, shifting the onus to defining traits worth emulating by pharmaceuticals, and searching phenotypically for people with these traits. This also shifts the question of what is rare or common from the many underlying causes to the possibility of a common final pathway.

Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by detection of N2 O released and nitrogen isotope determinations of fern biomass. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct nearly full-length Rhizobiales genomes were identified in leaf-pocket-enriched samples from ditch grown A. filiculoides. Their annotation revealed genes for denitrification but not N2 -fixation. 15 N2 incorporation was active in ferns with N. azollae but not in ferns without. N2 O was not detectably released from surface-sterilized ferns with the Rhizobiales. N2 -fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2 O.

Assemblies, orthology assignment and transcript abundance estimates for each species used in the paper titled "Wide sampling of natural diversity identifies conserved and novel molecular signatures of the highly complex trait C4 photosynthesis"

Optogenetic tools enable examination of how specific cell types contribute to brain circuit functions. A long-standing question is whether it is possible to independently activate two distinct neural populations in mammalian brain tissue. Such a capability would enable the study of how different synapses or pathways interact to encode information in the brain. Here we describe two channelrhodopsins, Chronos and Chrimson, discovered through sequencing and physiological characterization of opsins from over 100 species of alga. Chrimson's excitation spectrum is red shifted by 45 nm relative to previous channelrhodopsins and can enable experiments in which red light is preferred. We show minimal visual system-mediated behavioral interference when using Chrimson in neurobehavioral studies in Drosophila melanogaster. Chronos has faster kinetics than previous channelrhodopsins yet is effectively more light sensitive. Together these two reagents enable two-color activation of neural spiking and downstream synaptic transmission in independent neural populations without detectable cross-talk in mouse brain slice.

Includes presentation abstracts for authors listed as well as abstracts for posters by K. Marx, A. Kiehne, M. Meyer; Saifur R. Khan, Argishti Baghdasarian, Richard P. Fahlman, Arno G. Siraki; S.N. Reinke, D.I. Broadhurst, C. Power; Shereen A. Elbayomy, Mark T. McDermott; Simon Ng, Mohammad R. Jafari, Wadim Matochko, Ratmir Derda; A. F. El-Yazbi and G. R. Loppnow; Tania Nasreen, Paul C. Kirchberger and Yan Boucher; Argishti Baghdasarian, Saifur R. Khan, Richard Fahlman, Karim Michail, and Arno G. Siraki; Angela W.S. Fung, Devin K. Ulvestad, Aaron Madryga, Jack Moore, Richard P. Fahlman; Leslie D. Shewchuk, David Kramer and Dr. Richard P. Fahlman; Shaimaa Hussein and Xing-Zhen Chen; Julian C. A. Sacher, Braden T. Milan, Steven G. Chaulk, Richard P. Fahlman; Michal E. Gozdzik, Angela W.S. Fung, and Richard P. Fahlman; Wadim L. Matochko, Simon Ng, Mohammad R. Jafari, Sindy K.Y. Tang, Ratmir Derda; Steven G. Chaulk, Braden Millan, Richard P. Fahlman; Susan Koziel, Jim Davies, Karen Budwill, John Vidmar and Jian Zhang; Kirby A. Ziegler and D. Alan Underhill; Devin K. Ulvestad, Angela W.S. Fung, and Richard P. Fahlman; A Narasimhan, D Marks, T Braun, V Baracos and S Damaraju; P Krishnan, A Narasimhan, J Mackey, S Ghosh, O Kovalchuk and S Damaraju; Reza Jafari, Lu Deng, Simon Ng, Wadim L. Matochko, Anthony Zeberoff, Anastasia Elias, Pavel Kitov, John S. Klassen, Ratmir Derda; Elizabeth Nanak; Victor Cheng, Glen Zhang, Feifei Fu, Steve Oyedotun, Doug Ridgway, Mike Ellison, Liang Li, Joel H. Weiner; Stanislav Sokolenko, Ryan McKay, Eric JM Blondeel, Michael J Lewis, David Chang, Ben George, and Marc G Aucoin; Paige Lacy, Ryan McKay, Michael Finkel, Alla Karnovsky, Scott Woehler, David Chang, and Kathleen A. Stringer; Lars Laurentius and Mark T. McDermott; Harjot Atwal, Leen Labeeuw, Rebecca Case; Yahya Fiteih, Marilyn Gordon, Le Luong, and Shairaz Baksh; Constance Sobsey, Rupasri Mandal, Ram Krishnamurthy, Souhaila Bouatra, Igor Sinelnikov, An Chi Guo, Philip Liu, Kruti K. Chaudhary, Edison Dong, Farid Aziat, Faizath S. Yallou, Tom Blydt-Hansen, Ray Bahado-Singh and David S. Wishart; Ngoc Tran Tran, Roger A. Dixon and Liang Li; Jun Peng and Liang Li; Zhendong Li, Nan Wang and Liang Li; Ruokun Zhou, Chiao-Li Tseng, Liang Li; Feifei Fu, Yiman Wu, Victor Cheng, Joel Weiner, Liang Li; Difei Sun, Nan Wang, Liang Li; Chiao-Li Tseng, Michael Deyholos, Liang Li; Tao Huan, Wei Han, Ruokun Zhou and Liang Li; Yiman Wu, Liang Li; Stephen Pollo, Julia Foght and Camilla Nesbø; Camilla L. Nesbø, Kristen Swithers, Thomas Haverkamp, Olga Zhaxybayeva; Jared Curle and Liang Li; Harjot Atwal, Leen Labeeuw, Rebecca Case.

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.