Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to bemuch less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-living Lindenbergia. Following initial phylogenetic detection and an extensive validation procedure, 52 high-confidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence. Analyses of intron sequences in putative donor and recipient lineages provide evidence for integration of genomic fragments far more often than retro-processed RNA sequences. Purifying selection predominates in functionally transferred sequences, with a small fraction of adaptively evolving sites. HGT-acquired genes are preferentially expressed in the haustorium-the organ of parasitic plants-and are strongly biased in predicted gene functions, suggesting that expression products of horizontally acquired genes are contributing to the unique adaptive feeding structure of parasitic plants. ; NSF Equipment GrantNational Science Foundation (NSF) [MRI-1229046]; NSF Plant Genome Research ProgramNational Science Foundation (NSF)NSF - Office of the Director (OD) [DBI-0701748, IOS-1238057]; Plant Biology graduate program; Genetics graduate program; Biology Department at Penn State University; National Institute of Food and Agriculture Project [131997]; NSF GrantNational Science Foundation (NSF) [IOS-1213059] ; We thank Dr. Craig Praul and the Huck Genomics Core Facility for transcriptome sequencing and the gift of Striga genome sequences generated on a trial run of the Illumina HiSeq2500 sequencer that was purchased as NSF Equipment Grant MRI-1229046 (to C.W.d.); Tony Omeis for growing M. californica (with Grindelia host) in the Biology Greenhouse at Penn State University from material originally provided by Alison Colwell; K. Shirasu and S. Yoshida for access to the S. asiatica genome sequence and annotation; D. E. Soltis, M. K. Deyholos, M. W. Chase, and C. Wang for collecting nine of the 10 1KP samples used for HGT validation in this study; Ning Jiang (Michigan State University) for discussion of Pong-like TEs; and J. Naumann, J. Der, J. Palmer, M. Axtell, D. Cosgrove, S. Maximova, and M. Guiltinan for helpful suggestions. This research was supported by NSF Plant Genome Research Program Awards DBI-0701748 and IOS-1238057 (to J.H.W., C.W.d., M.P.T., and J.I.Y.), with additional support from the Plant Biology graduate program (Z.Y., L.A.H., S.J., and H.Z.) and from the Genetics graduate program as well as the Biology Department (Y.Z.) at Penn State University; National Institute of Food and Agriculture Project 131997 (to J.H.W.); and NSF Grant IOS-1213059 (to M.P.T.). ; Public domain authored by a U.S. government employee
Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns—one at the base of 'core leptosporangiates' and one specific to Azolla. One fernspecific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla–cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life. ; Partly supported by the Shenzhen Municipal Government of China (no. JCYJ20150529150409546), the National Science Foundation Doctoral Dissertation Improvement Grant DEB-1407158 (to K.M.P. and F.-W.L.) and the German Research Foundation Research Fellowship VR132/1-1 (to J.d.V.). ; http://www.nature.com/nplants ; am2018 ; Biochemistry ; Genetics ; Microbiology and Plant Pathology
Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innova-tions, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent. ; Publisher PDF ; Peer reviewed
Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent. ; Peer reviewed
In: Fazey , I , Schäpke , N , Caniglia , G , Hodgson , A , Kendrick , I , Lyon , C , Page , G , Patterson , J , Riedy , C , Strasser , T , Verveen , S , Adams , D , Goldstein , B , Klaes , M , Leicester , G , Linyard , A , McCurdy , A , Ryan , P , Sharpe , B , Silvestri , G , Abdurrahim , A Y , Abson , D , Adetunji , O S , Aldunce , P , Alvarez-Pereira , C , Amparo , J M , Amundsen , H , Anderson , L , Andersson , L , Asquith , M , Augenstein , K , Barrie , J , Bent , D , Bentz , J , Bergsten , A , Berzonsky , C , Bina , O , Blackstock , K , Boehnert , J , Bradbury , H , Brand , C , Böhme (born Sangmeister) , J , Bøjer , M M , Carmen , E , Charli-Joseph , L , Choudhury , S , Chunhachoti-ananta , S , Cockburn , J , Colvin , J , Connon , I L C , Cornforth , R , Cox , R S , Cradock-Henry , N , Cramer , L , Cremaschi , A , Dannevig , H , Day , C T , de Lima Hutchison , C , de Vrieze , A , Desai , V , Dolley , J , Duckett , D , Durrant , R A , Egermann , M , Elsner (Adams) , E , Fremantle , C , Fullwood-Thomas , J , Galafassi , D , Gobby , J , Golland , A , González-Padrón , S K , Gram-Hanssen , I , Grandin , J , Grenni , S , Lauren Gunnell , J , Gusmao , F , Hamann , M , Harding , B , Harper , G , Hesselgren , M , Hestad , D , Heykoop , C A , Holmén , J , Holstead , K , Hoolohan , C , Horcea-Milcu , A I , Horlings , L G , Howden , S M , Howell , R A , Huque , S I , Inturias Canedo , M L , Iro , C Y , Ives , C D , John , B , Joshi , R , Juarez-Bourke , S , Juma , D W , Karlsen , B C , Kliem , L , Kläy , A , Kuenkel , P , Kunze , I , Lam , D P M , Lang , D J , Larkin , A , Light , A , Luederitz , C , Luthe , T , Maguire , C , Mahecha-Groot , A M , Malcolm , J , Marshall , F , Maru , Y , McLachlan , C , Mmbando , P , Mohapatra , S , Moore , M L , Moriggi , A , Morley-Fletcher , M , Moser , S , Mueller , K M , Mukute , M , Mühlemeier , S , Naess , L O , Nieto-Romero , M , Novo , P , ÓBrien , K , O'Connell , D A , O'Donnell , K , Olsson , P , Pearson , K R , Pereira , L , Petridis , P , Peukert , D , Phear , N , Pisters , S R , Polsky , M , Pound , D , Preiser , R , Rahman , M S , Reed , M S , Revell , P , Rodriguez , I , Rogers , B C , Rohr , J , Nordbø Rosenberg , M , Ross , H , Russell , S , Ryan , M , Saha , P , Schleicher , K , Schneider , F , Scoville-Simonds , M , Searle , B , Sebhatu , S P , Sesana , E , Silverman , H , Singh , C , Sterling , E , Stewart , S J , Tàbara , J D , Taylor , D , Thornton , P , Tribaldos , T M , Tschakert , P , Uribe-Calvo , N , Waddell , S , Waddock , S , van der Merwe , L , van Mierlo , B , van Zwanenberg , P , Velarde , S J , Washbourne , C L , Waylen , K , Weiser , A , Wight , I , Williams , S , Woods , M , Wolstenholme , R , Wright , N , Wunder , S , Wyllie , A & Young , H R 2020 , ' Transforming knowledge systems for life on Earth : Visions of future systems and how to get there ' , Energy Research and Social Science , vol. 70 , 101724 . https://doi.org/10.1016/j.erss.2020.101724
Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) 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. ; Alberta Ministry of Advanced Education; Alberta Innovates AITF/iCORE Strategic Chair [RES0010334]; Musea Ventures; National Key Research and Development Program of China [2016YFE0122000]; Ministry of Science and Technology of the People's Republic of ChinaMinistry of Science and Technology, China [2015BAD04B01/2015BAD04B03]; State Key Laboratory of Agricultural Genomics [2011DQ782025]; Guangdong Provincial Key Laboratory of core collection of crop genetic resources research and application [2011A091000047]; Shenzhen Municipal Government of China [CXZZ20140421112021913/JCYJ20150529150409546/JCYJ20150529150505656]; National Science FoundationNational Science Foundation (NSF) [DBI-1265383, IOS 0922742, IOS-1339156, DEB 0830009, EF-0629817, EF-1550838, DEB 0733029, DBI 1062335, 1461364]; National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [1R01DA025197]; Deutsche ForschungsgemeinschaftGerman Research Foundation (DFG) [Qu 141/5-1, Qu 141/6-1, GR 3526/7-1, GR 3526/8-1]; Natural Sciences and Engineering Research Council of CanadaNatural Sciences and Engineering Research Council of Canada ; The 1KP initiative was funded by the Alberta Ministry of Advanced Education and Alberta Innovates AITF/iCORE Strategic Chair (RES0010334) to G.K.-S.W., Musea Ventures, The National Key Research and Development Program of China (2016YFE0122000), The Ministry of Science and Technology of the People's Republic of China (2015BAD04B01/2015BAD04B03), the State Key Laboratory of Agricultural Genomics (2011DQ782025) and the Guangdong Provincial Key Laboratory of core collection of crop genetic resources research and application (2011A091000047). Sequencing activities at BGI were also supported by the Shenzhen Municipal Government of China (CXZZ20140421112021913/JCYJ20150529150409546/JCYJ20150529150505656). Computation support was provided by the China National GeneBank (CNGB), the Texas Advanced Computing Center (TACC), WestGrid and Compute Canada; considerable support, including personnel, computational resources and data hosting, was also provided by the iPlant Collaborative (CyVerse) funded by the National Science Foundation (DBI-1265383), National Science Foundation grants IOS 0922742 (to C.W.d., P.S.S., D.E.S. and J.H.L.-M.), IOS-1339156 (to M.S.B.), DEB 0830009 (to J.H.L.-M., C.W.d., S.W.G. and D.W.S.), EF-0629817 (to S.W.G. and D.W.S.), EF-1550838 (to M.S.B.), DEB 0733029 (to T.W. and J.H.L.-M.), and DBI 1062335 and 1461364 (to T.W.), a National Institutes of Health Grant 1R01DA025197 (to T.M.K., C.W.d. and J.H.L.-M.), Deutsche Forschungsgemeinschaft grants Qu 141/5-1, Qu 141/6-1, GR 3526/7-1, GR 3526/8-1 (to M.Q. and I.G.) and a Natural Sciences and Engineering Research Council of Canada Discovery grant (to S.W.G.). We thank all national, state, provincial and regional resource management authorities, including those of province Nord and province Sud of New Caledonia, for permitting collections of material for this research. ; Public domain authored by a U.S. government employee
Background: The COVID-19 pandemic has disrupted routine hospital services globally. This study estimated the total number of adult elective operations that would be cancelled worldwide during the 12 weeks of peak disruption due to COVID-19. Methods: A global expert response study was conducted to elicit projections for the proportion of elective surgery that would be cancelled or postponed during the 12 weeks of peak disruption. A Bayesian β-regression model was used to estimate 12-week cancellation rates for 190 countries. Elective surgical case-mix data, stratified by specialty and indication (surgery for cancer versus benign disease), were determined. This case mix was applied to country-level surgical volumes. The 12-week cancellation rates were then applied to these figures to calculate the total number of cancelled operations. Results: The best estimate was that 28 404 603 operations would be cancelled or postponed during the peak 12 weeks of disruption due to COVID-19 (2 367 050 operations per week). Most would be operations for benign disease (90·2 per cent, 25 638 922 of 28 404 603). The overall 12-week cancellation rate would be 72·3 per cent. Globally, 81·7 per cent of operations for benign conditions (25 638 922 of 31 378 062), 37·7 per cent of cancer operations (2 324 070 of 6 162 311) and 25·4 per cent of elective caesarean sections (441 611 of 1 735 483) would be cancelled or postponed. If countries increased their normal surgical volume by 20 per cent after the pandemic, it would take a median of 45 weeks to clear the backlog of operations resulting from COVID-19 disruption. Conclusion: A very large number of operations will be cancelled or postponed owing to disruption caused by COVID-19. Governments should mitigate against this major burden on patients by developing recovery plans and implementing strategies to restore surgical activity safely.