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1. Tricin-lignins: occurrence and quantitation of tricin in relation to phylogeny.

Author

Lan W, Rencoret J, Lu F, Karlen SD, Smith BG, Harris PJ, Del Río JC, and Ralph J

Subjects
Chromatography, Liquid, Mass Spectrometry, Poaceae classification, Poaceae metabolism, Flavonoids metabolism, Lignin metabolism, Phylogeny
Abstract

Tricin [5,7-dihydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-4H-chromen-4-one], a flavone, was recently established as an authentic monomer in grass lignification that likely functions as a nucleation site. It is linked onto lignin as an aryl alkyl ether by radical coupling with monolignols or their acylated analogs. However, the level of tricin that incorporates into lignin remains unclear. Herein, three lignin characterization methods: acidolysis; thioacidolysis; and derivatization followed by reductive cleavage; were applied to quantitatively assess the amount of lignin-integrated tricin. Their efficiencies at cleaving the tricin-(4'-O-β)-ether bonds and the degradation of tricin under the corresponding reaction conditions were evaluated. A hexadeuterated tricin analog was synthesized as an internal standard for accurate quantitation purposes. Thioacidolysis proved to be the most efficient method, liberating more than 91% of the tricin with little degradation. A survey of different seed-plant species for the occurrence and content of tricin showed that it is widely distributed in the lignin from species in the family Poaceae (order Poales). Tricin occurs at low levels in some commelinid monocotyledon families outside the Poaceae, such as the Arecaceae (the palms, order Arecales) and Bromeliaceae (Poales), and the non-commelinid monocotyledon family Orchidaceae (Orchidales). One eudicotyledon was found to have tricin (Medicago sativa, Fabaceae). The content of lignin-integrated tricin is much higher than the extractable tricin level in all cases. Lignins, including waste lignin streams from biomass processing, could therefore provide a large and alternative source of this valuable flavone, reducing the costs, and encouraging studies into its application beyond its current roles., (© 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Published
2016
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2. An aquaglyceroporin is abundantly expressed early in the development of the suspensor and the embryo proper of loblolly pine.

Author

Ciavatta VT, Morillon R, Pullman GS, Chrispeels MJ, and Cairney J

Subjects
Amino Acid Sequence, Animals, Aquaporins metabolism, Cloning, Molecular, Eukaryotic Initiation Factor-3, Female, Fungal Proteins genetics, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Glycerol metabolism, Immediate-Early Proteins genetics, Ion Channels genetics, Membrane Proteins genetics, Molecular Sequence Data, Nuclear Proteins genetics, Oocytes, Osmotic Pressure, Pinus growth & development, Pinus taeda, Plant Proteins genetics, RNA, Messenger genetics, RNA, Messenger metabolism, Saccharomyces cerevisiae genetics, Seeds growth & development, Sequence Homology, Amino Acid, Serine Endopeptidases genetics, Xenopus laevis genetics, Aquaporins genetics, Phylogeny, Pinus genetics, Saccharomyces cerevisiae Proteins, Seeds genetics
Abstract

In contrast to angiosperms, pines and other gymnosperms form well-developed suspensors in somatic embryogenic cultures. This creates a useful system to study suspensor biology. In a study of gene expression during the early stages of conifer embryogenesis, we identified a transcript, PtNIP1;1, that is abundant in immature loblolly pine (Pinus taeda) zygotic and somatic embryos, but is undetectable in later-stage embryos, megagametophytes, and roots, stems, and needles from 1 year-old seedlings. Analysis of PtNIP1;1 transcript in embryo proper and suspensor tissues by reverse transcription-polymerase chain reaction suggests preferential expression in the suspensor. Based on comparisons of derived amino acid sequences, PtNIP1;1 belongs to the nodulin-like members of the major intrinsic protein superfamily branch of the aquaporin (major intrinsic protein) superfamily. Through heterologous expression in Xenopus laevis oocytes and the yeast (Saccharomyces cerevisiae) fps1(-) mutant, PtNIP1;1 has been shown to be an active aquaglyceroporin.

Published
2001

3. Ignicoccus hospitalis sp. nov., the host of 'Nanoarchaeum equitans'

Author

Walter Paper, Ulrike Jahn, Karl O. Stetter, Tillmann Burghardt, Daniela J. Näther, Harald Huber, Michael J. Hohn, Reinhard Rachel, and Michaela Kronner

Subjects
Genetics, Base Composition, Chemoautotrophic Growth, Phylogenetic tree, Ignicoccus, Desulfurococcaceae, Molecular Sequence Data, Iceland, Zoology, Membrane Proteins, General Medicine, Genus Ignicoccus, Biology, biology.organism_classification, Microbiology, Phylogenetics, Ignicoccus islandicus, Nanoarchaeota, Nanoarchaeum equitans, Taxonomy (biology), Ecology, Evolution, Behavior and Systematics, Phylogeny
Abstract

A novel chemolithoautotrophic and hyperthermophilic member of the genus Ignicoccus was isolated from a submarine hydrothermal system at the Kolbeinsey Ridge, to the north of Iceland. The new isolate showed high similarity to the two species described to date, Ignicoccus islandicus and Ignicoccus pacificus, in its physiological properties as well as in its unique cell architecture. However, phylogenetic analysis and investigations on the protein composition of the outer membrane demonstrated that the new isolate was clearly distinct from I. islandicus and I. pacificus. Furthermore, it is the only organism known so far which is able to serve as a host for ‘Nanoarchaeum equitans’, the only cultivated member of the ‘Nanoarchaeota’. Therefore, the new isolate represents a novel species of the genus Ignicoccus, which we name Ignicoccus hospitalis sp. nov. (type strain KIN4/IT=DSM 18386T=JCM 14125T).

Published
2007

4. The challenge of West Nile virus in Europe: knowledge gaps and research priorities

Author

Sebastian Ulbert, Norbert Nowotny, Ana Moreno, Luisa Barzon, N. Pardigon, Penelope Koraka, Antonio Tenorio, Miguel Ángel Jiménez-Clavero, Jordi Figuerola, Paolo Cordioli, Niek N. Sanders, Byron E. E. Martina, Annapaola Rizzoli, Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Centro de Investigacion en Sanidad Animal (INIA-CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Universita degli Studi di Padova, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna 'Bruno Ubertini' (IZSLER), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Erasmus University Medical Center [Rotterdam] (Erasmus MC), University of Veterinary Medicine [Vienna] (Vetmeduni), Sultan Qaboos University (SQU), Institut Pasteur [Paris], Universiteit Gent = Ghent University [Belgium] (UGENT), Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI), Fraunhofer (Fraunhofer-Gesellschaft), Instituto de Salud Carlos III [Madrid] (ISC), This paper is the product of a cooperative action promoted by the Coordinators and delegates of the EU funded projects on West Nile virus under the 7th European Programme, in particular the EuroWestNile project (www.eurowestnile.org, GA n. 261391), the EDENext project (www.edenext.eu , GA n. 261504) the Wings project (www.west-nile-shield-project.eu , GA n. 261426), and the Vectorie project (www.vectorie.eu , GA n. 261466). This study was partially funded by EU grant FP7-261504 EDENext and is catalogued by the EDENext Steering Committee as EDENext 142 (http://www.edenext.eu). AR was partially funded by the Autonomous Province of Trento grant LExEM (http://www.lexem.eu). The contents of this publication are the sole responsibility of the authors and don't necessarily reflect the views of the European Commission., This paper is dedicated to the memory of our wonderful colleague and friend, Dr Paolo Cordioli, who recently passed away. We thank the European Centre for Disease Prevention and Control (ECDC) for supporting this initiative and for promoting a stronger integration between public health and research in Europe. We also thank Dr Jolanta Kolodziejek of the Institute of Virology, University of Veterinary Medicine Vienna for establishing the phylogenetic trees and Matteo Marcantonio of the GIS/RS platform at the Edmund Mach Foundation for preparing the map in Figure 1, European Project: 261391,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EUROWESTNILE(2011), European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), European Project: 261426,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,WINGS(2011), European Project: 261466,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,VECTORIE(2010), Virology, Università degli Studi di Padova = University of Padua (Unipd), Institut Pasteur [Paris] (IP), Universiteit Gent = Ghent University (UGENT), and Publica

Subjects
Health Knowledge, Attitudes, Practice, Veterinary medicine, Economic growth, WNV STRAINS, Epidemiology, viruses, MESH: Health Knowledge, Attitudes, Practice, medicine.disease_cause, Disease Outbreaks, EXPERIMENTAL-INFECTION, ENVELOPE PROTEIN, Neuroinvasive disease, Medicine and Health Sciences, MESH: Genetic Variation, MESH: Disease Outbreaks, MESH: Phylogeny, Phylogeny, media_common, EARLY WARNING SYSTEM, biology, SUBSTITUTION, AMINO-ACID, 3. Good health, Europe, MESH: Research, Geography, Population Surveillance, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, West Nile virus, SPARROWS PASSER-DOMESTICUS, media_common.quotation_subject, Ecology (disciplines), MESH: Population Surveillance, SDG 3 - Good Health and Well-being, Virology, medicine, Humans, media_common.cataloged_instance, Veterinary Sciences, European union, TIME RT-PCR, Settore VET/06 - PARASSITOLOGIA E MALATTIE PARASSITARIE DEGLI ANIMALI, MESH: West Nile virus, MESH: West Nile Fever, MESH: Humans, Research, LINEAGE 1 STRAIN, Public Health, Environmental and Occupational Health, Genetic Variation, Outbreak, biology.organism_classification, USUTU VIRUS, Early warning system, MESH: Europe, CULEX-PIPIENS MOSQUITOS, Usutu virus, West Nile Fever, Diversity (politics)
Abstract

West Nile virus (WNV) is continuously spreading across Europe, and other continents, i.e. North and South America and many other regions of the world. Despite the overall sporadic nature of outbreaks with cases of West Nile neuroinvasive disease (WNND) in Europe, the spillover events have increased and the virus has been introduced into new areas. The high genetic diversity of the virus, with remarkable phenotypic variation, and its endemic circulation in several countries, require an intensification of the integrated and multidisciplinary research efforts built under the 7th Framework Programme of the European Union (FP7). It is important to better clarify several aspects of WNV circulation in Europe, including its ecology, genomic diversity, pathogenicity, transmissibility, diagnosis and control options, under different environmental and socio-economic scenarios. Identifying WNV endemic as well as infection-free areas is becoming a need for the development of human vaccines and therapeutics and the application of blood and organs safety regulations. This review, produced as a joint initiative among European experts and based on analysis of 118 scientific papers published between 2004 and 2014, provides the state of knowledge on WNV and highlights the existing knowledge and research gaps that need to be addressed with high priority in Europe and neighbouring countries.

Published
2015

5. Presence of Recombinant Bat Coronavirus GCCDC1 in Cambodian Bats

Author

Feng Zhu, Veasna Duong, Xiao Fang Lim, Vibol Hul, Tanu Chawla, Lucy Keatts, Tracey Goldstein, Alexandre Hassanin, Vuong Tan Tu, Philippe Buchy, October M. Sessions, Lin-Fa Wang, Philippe Dussart, Danielle E. Anderson, Duke-NUS Medical School [Singapore], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Wildlife Conservation Society (WCS), University of California [Davis] (UC Davis), University of California (UC), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Vietnam Academy of Science and Technology (VAST), University of Melbourne, and DEA and L-FW were supported by Grants NRF2012NRFCRP001-056 and NRF2016NRF-NSFC002-013 from the Singapore National Research Foundation. This study was made possible by the generous support of the American people through the United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICT project (cooperative agreement number GHN-A-OO-09-00010-00 and AID-OAA-A-14-00102). The contents of this paper are the responsibility of the authors and do not necessarily reflect the views of the US Agency for International Development or the US Government. The fieldwork was supported in part by the National Authority for Preah Vihear, UNESCO, 'Société des amis du Muséum et du Jardin des Plantes', and the Muséum national d’Histoire naturelle.

Subjects
Recombination, Genetic, China, Coronaviridae, Coronaviridae Infections, [SDV]Life Sciences [q-bio], viruses, bats, coronavirus, virus diseases, cross-species transmission, Genome, Viral, zoonosis, recombination, respiratory tract diseases, Evolution, Molecular, Phylogeography, co-infection, Infectious Diseases, Chiroptera, Virology, Animals, GCCDC1, Cambodia, Phylogeny, Disease Reservoirs
Abstract

International audience; Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia.

Published
2022

6. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

Author

Panagiotis S. Adam, Simonetta Gribaldo, Guillaume Borrel, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), P.S.A. is supported by a PhD fellowship from Paris Diderot University and by funds from the PhD Programme 'Frontières du Vivant (FdV)–Programme Bettencourt.' G.B. is a recipient of a Roux-Cantarini fellowship from the Institut Pasteur. S.G. acknowledges funding from the French National Agency for Research Grant ArchEvol (ANR-16-CE02-0005-01)., We thank Alexander Probst for feedback on an earlier version of the paper, and two anonymous reviewers whose comments helped improve clarity and correctness of the manuscript., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), and Institut Pasteur [Paris]

Subjects
0301 basic medicine, Enzyme complex, MESH: Genome, Archaeal, LUCA, [SDV]Life Sciences [q-bio], MESH: Genome, Bacterial, Genome, Corrections, chemistry.chemical_compound, Genome, Archaeal, MESH: Multienzyme Complexes/genetics, methanogens, Phylogeny, MESH: Phylogeny, Genetics, Carbon Monoxide, Multidisciplinary, Last universal ancestor, Carbon fixation, Acetyl-CoA, MESH: Carbon Cycle, Aldehyde Oxidoreductases, Biological Evolution, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, PNAS Plus, MESH: Bacteria/enzymology, Wood–Ljungdahl pathway, Wood-Ljungdahl pathway, MESH: Aldehyde Oxidoreductases/metabolism, Carbon monoxide dehydrogenase, 030106 microbiology, MESH: Bacteria/genetics, Acetate-CoA Ligase, Bacterial genome size, Biology, MESH: Biological Evolution, MESH: Aldehyde Oxidoreductases/genetics, Carbon Cycle, 03 medical and health sciences, MESH: Carbon Monoxide/metabolism, Multienzyme Complexes, MESH: Archaea/genetics, evolution, MESH: Acetate-CoA Ligase/metabolism, MESH: Multienzyme Complexes/metabolism, MESH: Archaea/enzymology, Bacteria, MESH: Acetate-CoA Ligase/genetics, Archaea, acetogens, 030104 developmental biology, chemistry, biology.protein, Genome, Bacterial
Abstract

Erratum in : Correction for Adam et al., Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. [Proc Natl Acad Sci U S A. 2018]; International audience; Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of un-cultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal-bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.

Published
2018

7. Genome-scale rates of evolutionary change in bacteria

Author

Jane Hawkey, David J. Edwards, Simon Le Hello, Kathryn E. Holt, Mathieu Fourment, Edward C. Holmes, François-Xavier Weill, Sebastián Duchêne, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Centre for Systems Genomics, The University of MelbourneParkville, VIC, Australia., Department of Biochemistry and Molecular Biology, Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella (CNR-ESS), Institut Pasteur [Paris] (IP), This research was funded by the NHMRC (Australia Fellowship#AF30 to E. C. H., Career Development Fellowship #1061409 toK. E. H.). S. D. was supported by a McKenzie fellowship from the University of Melbourne.This paper was supported by the following grant(s):National Health and Medical Research Council 1061409.National Health and Medical Research Council GNT1037231., and Institut Pasteur [Paris]

Subjects
0301 basic medicine, 0106 biological sciences, Mechanisms of Evolution, Evolutionary change, Genome scale, Bacterial genome size, phylogeny, Genome, 010603 evolutionary biology, 01 natural sciences, Orders of magnitude (bit rate), Evolution, Molecular, 03 medical and health sciences, Phylogenetics, evolution, Molecular clock, Evolutionary dynamics, 030304 developmental biology, Whole genome sequencing, Genetics, 0303 health sciences, biology, Bacteria, Models, Genetic, molecular clock, Genetic Variation, General Medicine, biology.organism_classification, Biological Evolution, 030104 developmental biology, Ancient DNA, 13. Climate action, Evolutionary biology, time-dependency, Microbial Evolution and Epidemiology, Mutation, Human genome, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, substitution rates, Genome, Bacterial, Research Paper
Abstract

Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations, and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with “ancient DNA” data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from 10−6 to 10−8 nucleotide substitutions site-1 year-1. This variation was largely attributable to sampling time, which was strongly negatively associated with estimated evolutionary rates, with this relationship best described by an exponential decay curve. To avoid potential estimation biases such time-dependency should be considered when inferring evolutionary time-scales in bacteria.

Published
2016

8. The genome of Eucalyptus grandis

Author

Anand Raj Kumar Kullan, Erich Bornberg-Bauer, Christopher M. Sullivan, Florent Murat, Elisson Romanel, Yves Van de Peer, Aaron Liston, Priya Ranjan, Dorothy A. Steane, Justin Elser, Pooja Singh, Victor Carocha, Orzenil B. Silva-Junior, Marçal Soler, Cesar Petroli, Inna Dubchak, Jane Grimwood, Carsten Külheim, Danielle A. Faria, Ida Van Jaarsveld, Chu-Yu Ye, Giancarlo Pasquali, Charles A. Hefer, Desre Pinard, Roberto C. Togawa, Richard D. Hayes, Eshchar Mizrachi, Fourie Joubert, Erika Lindquist, Kevin Vanneste, Philippe Rigault, Jérôme Salse, Karen Van der Merwe, David Kudrna, Palitha Dharmwardhana, Gerald A. Tuskan, Diane Bauer, Alexandre Poliakov, Marcio Alves-Ferreira, Kerrie Barry, Vindhya Amarasinghe, Ting Li, William J. Foley, Georgios J. Pappas, Carolina Sansaloni, René E. Vaillancourt, Marília de Castro Rodrigues Pappas, Uffe Hellsten, Daniel S. Rokhsar, Martin Ranik, Anna R. Kersting, Alexander Andrew Myburg, Hua Cassan-Wang, David Goodstein, Christophe Dunand, Naijib Saidi, Timothy J. Tschaplinski, Sushma Naithani, Dario Grattapaglia, Pankaj Jaiswal, Steven G. Hussey, Jeremy Schmutz, Rajani Raja, Brad M. Potts, Margaret Byrne, Antanas V. Spokevicius, Jorge A. P. Paiva, Jacqueline Grima-Pettenati, Xiaohan Yang, Alexander Boyd, Hope Tice, Joseph W. Spatafora, Lieven Sterck, Jerry Jenkins, Steven H. Strauss, Sérgio Hermínio Brommonschenkel, Josquin Tibbits, Rebecca C. Jones, Kelly J. Vining, Hélène San Clemente, BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, DOE Joint Genome Institute [Walnut Creek], Department of Epidemiology & Population Health, London School of Hygiene and Tropical Medicine (LSHTM), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), United States Department of Energy, US Department of Energy Joint Genome Institute, University of California, Embrapa Uva e Vinho (BRAZIL), Technicolor R & I [Cesson Sévigné], Technicolor, Department of Plant Systems Biology, State University of Ghent, Ghent University [Belgium] (UGENT), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institute for Evolution and Biodiversity (IEB), Westfälische Wilhelms-Universität Münster (WWU), Department of Botany and Plant Pathology, Oregon State University (OSU), RAIZ – Forestry & Paper Research Institut, Laboratory of Plant Cell Biotechnology, ITQB/IBET, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, GYDLE, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bioinformatics and Computational Biology Unit, Faculty of Natural and Agricultural Sciences-University of Pretoria [South Africa], Institute of Continuing Medical Education of Ioannina, Plastes et différenciation cellulaire (PDC), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Universiteit Gent = Ghent University [Belgium] (UGENT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Régulation et Dynamique de la Formation du Bois, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Dynamique et Evolution des Parois cellulaires végétales, Office of Science of the US Department of Energy [DE-AC02-05CH11231], Office of Biological and Environmental Research in the US Department of Energy Office of Science, US DOE Bioenergy Center [DE-AC05-00OR22725], Brazilian Ministry of Science, Technology and Innovation (MCTI) through (CNPq), Brazilian Ministry of Science, Technology and Innovation (MCTI) through (FINEP), Brazilian Federal District Research Foundation (FAP-DF), Technology and Human Resources for Industry Programme (THRIP) [UID 80118], South African Department of Science and Technology (DST), National Research Foundation (NRF) [UID 18312, 86936], Laboratoire d'Excellence [LABEX TULIP ANR-10-LABX-41], Agence Nationale pour la Recherche (Project Tree For Joules) [ANR-2010-KBBE-007-01], Fundacao para a Ciencia e Tecnologia (FCT) [P-KBBE/AGR_GPL/0001/2010], Centre National pour la Recherche Scientifique (CNRS), University Paul Sabatier Toulouse III (UPS), Ghent University, Hercules Foundation, Flemish Government-department EWI, Myburg, Alexander A., University of California (UC), Universiteit Gent = Ghent University (UGENT), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Westfälische Wilhelms-Universität Münster = University of Münster (WWU)

Subjects
Genome evolution, DATABASE, phylogénomique, [SDV]Life Sciences [q-bio], Biology, Genome, DNA sequencing, Evolution, Molecular, Phylogenomics, Myrtales, Botany, Inbreeding depression, TOOL, Inbreeding, RNA-SEQ, PLANT, NUCLEAR-DNA, Phylogeny, ComputingMilieux_MISCELLANEOUS, Eucalyptus, Multidisciplinary, FOREST TREES, Biology and Life Sciences, Genetic Variation, métabolisme secondaire, 15. Life on land, biology.organism_classification, GENE, EVOLUTION, ALIGNMENT, biocarburant, Biofuels, Eucalyptus globulus, évolution du génome, WHOLE-GENOME, Secondary metabolism, Genome, Plant
Abstract

International audience; Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

Published
2014

9. DNA barcoding in the rust genus Chrysomyxa and its implications for the phylogeny of the genus

Author

Wolfgang Maier, Mathieu Allaire, Richard C. Hamelin, Agathe Vialle, Nicolas Feau, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Natural Resources Canada (NRCan), Centre d’étude de la forêt, Université Laval [Québec] (ULaval), Ruhr University Bochum (RUB), University of British Columbia (UBC), and This paper is dedicated to Patricia Crane, our colleague deceased in 2010, who was a dedicated urediniologist and who contributed her knowledge and samples to this publication. We thank Dr Scott A. Redhead and Louise Lefebvre from the National Mycological Herbarium and Pierre DesRochers from Natural Resources Canada for kindly providing important herbarium strains, Marie-Josee Bergeron and Isabelle Lamarre from Natural Resources Canada for constructive comments on the manuscript This research was financially supported through the Canadian Barcode of Life Research Network from Genome Canada through the Ontario Genomics Institute, Natural Sciences and Engineering Research of Canada, and other sponsors at www.BOLNET.org.

Subjects
0106 biological sciences, 0301 basic medicine, Species complex, Physiology, Chrysomyxa pyrolae, phylogeny, 010603 evolutionary biology, 01 natural sciences, DNA barcoding, 03 medical and health sciences, Genus, Botany, DNA, Ribosomal Spacer, Genetics, medicine, DNA barcode, mitochondrial heteroplasmon, Internal transcribed spacer, fungal pathogen, DNA, Fungal, species complex, Molecular Biology, Ecology, Evolution, Behavior and Systematics, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Electronic Data Processing, Coleosporium, biology, Basidiomycota, cone rusts, Cell Biology, General Medicine, 030108 mycology & parasitology, 15. Life on land, biology.organism_classification, Chrysomyxa, chrysomyxa needle rusts, medicine.drug_formulation_ingredient, Chrysomyxa ledi, mycology
Abstract

International audience; Chrysomyxa rusts are fungal pathogens widely present in the boreal forest. Taxonomic delimitation and precise species identification are difficult within this genus because several species display similar morphological features. We applied a DNA barcode system based on the ribosomal internal transcribed spacer region (ITS), large subunit (28S) ribosomal RNA gene, mitochondrial cytochrome oxidase 1 (CO1) and mitochondrial NADH dehydrogenase subunit 6 (NAD6) in 86 strains from 16 different Chrysomyxa species, including members of the Chrysomyxa ledi species complex. The nuclear ITS and 28S loci revealed higher resolving power than the mitochondrial genes. Amplification of the full CO1 barcode region failed due to the presence of introns limiting the dataset obtained with this barcode. In most cases the ITS barcodes were in agreement with taxonomic species based on phenotypic characters. Nevertheless we observed genetically distinct (different DNA barcodes) lineages within Chrysomyxa pyrolae and Chrysomyxa rhododendri, providing some evidence for allopatric speciation within these morphologically defined species. This finding, together with the observed pattern of host specificities of the studied rust fungi, suggest that species diversification within the C. ledi species complex might be governed by a set of factors such as specialisation to certain Ericaceae species as telial hosts and to a lesser extent specialization to different spruce species as aecial hosts. Moreover allopatric speciation by geographic disruption of species also seems to take place. When our data were integrated into a broader phylogenetic framework the Chrysomyxa genus unexpectedly was not resolved as a monophyletic group. Indeed the spruce cone rusts C. pyrolae and C. monesis coalesced with the pine needle rusts belonging to the genus Coleosporium, whereas the microcyclic species Chrysomyxa weirii was embedded within a clade comprising the genus Melampsora.

Published
2011

10. Mucin CYS domains are ancient and highly conserved modules that evolved in concert

Author

Jean-Luc Desseyn, Lille Inflammation Research International Center - U 995 (LIRIC), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Institut de médecine predictive et de recherche thérapeutique (IMPRT), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Centre Régional de Lutte contre le Cancer Oscar Lambret [Lille] (UNICANCER/Lille), Université Lille Nord de France (COMUE)-UNICANCER-Université Lille Nord de France (COMUE)-UNICANCER-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Droit et Santé-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Université Lille 2 - Faculté de Médecine, The author gratefully acknowledges Dr. V. Gouyer (INSERM U795 and EA3925, Lille, France) and Pr. F. Gottrand (EA3925, University of Lille, France) for their critical comments. The author is indebted to Dr. P. Amieux (University of Washington, Seattle, WA) for help in improving the style of the paper., Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Université de Lille-UNICANCER-Université de Lille-UNICANCER-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Droit et Santé-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Faculté de Médecine Henri Warembourg - Université de Lille, and Lille Inflammation Research International Center - U 995 [LIRIC]

Subjects
MESH: Sequence Analysis, DNA, Animals, Conserved Sequence, Cysteine, Evolution, Molecular, Exons, Humans, Mucins, Phylogeny, Protein Interaction Domains and Motifs, Sequence Alignment, Sequence Analysis, DNA, [SDV]Life Sciences [q-bio], CYS domain, Genome, MUC5B, Exon, 0302 clinical medicine, Gel-forming mucin, MESH: Animals, MESH: Phylogeny, Genetics, 0303 health sciences, Concerted evolution, MESH: Conserved Sequence, Biochemistry, Coding repeats, MESH: Sequence Alignment, Biology, Evolution, Molecular, 03 medical and health sciences, MESH: Evolution, Molecular, MESH: Mucins/genetics, Amino acid residue, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Protein Interaction Domains and Motifs, MESH: Humans, MESH: Mucins/metabolism, Mucin, Sequence Analysis, DNA, MUC5AC, MESH: Cysteine/genetics, Mucus, MUC2, MESH: Exons, 030217 neurology & neurosurgery, Function (biology)
Abstract

International audience; Background : Many large secreted gel-forming mucins contain multiple copies of a "naked" cysteine-enriched domain (CYS domain) that interrupt or are adjacent to mucin domains (Ser/Thr/Pro regions). There is less similarity of homologous CYS sequences between species than there is across CYS repeats within species. These CYS domains are likely implicated in reversible mucin-mucin interactions that play a central role in mucus properties. Results : The use of multiple genome sequences in a comparative analysis of CYS sequences identified new mucins containing the CYS domain in various species. Furthermore, analysis showed that this domain is at least 650 million-year old and that CYS sequences evolved under strong selective pressure in concerted fashion in all species examined by two mechanisms that never coexist within a given gene: either multiplication of exons encoding CYS modules or successive intra-exonic duplications. Conclusion : The CYS sequences appear to have undergone concerted evolution with a high selective pressure to conserve cysteine and other amino acid residues. This domain is the best-conserved domain in secreted mucins pointing toward an important common function in many different organisms.

Published
2008

11. Characterization of Staphylococcus aureus strains associated with food poisoning outbreaks in France

Author

Jacques-Antoine Hennekinne, Annaëlle Kerouanton, L. Petit, C. Letertre, Anne Brisabois, O. Chesneau, M.L. De Buyser, Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Agents antibactériens, Institut Pasteur [Paris], We acknowledge the technical assistance of Trinh Tam Dao, Marie-Odile Delbart, Muriel Marault, and Anne Morvan. We dedicate this paper to the memory of Névine El Solh who contributed to the phage-typing and who passed away in January 2005., and Institut Pasteur [Paris] (IP)

Subjects
Salmonella, Enterotoxin, MESH: Base Sequence, medicine.disease_cause, SmaI, Disease Outbreaks, MESH: Genotype, Enterotoxins, Genotype, MESH: Staphylococcus aureus, MESH: Enterotoxins, Cluster Analysis, MESH: Disease Outbreaks, MESH: Phylogeny, Phylogeny, 2. Zero hunger, 0303 health sciences, General Medicine, PFGE, 3. Good health, Electrophoresis, Gel, Pulsed-Field, Phenotype, MESH: Electrophoresis, Gel, Pulsed-Field, Staphylococcus aureus, MESH: Staphylococcal Food Poisoning, France, Staphylococcal Food Poisoning, Food Contamination, Biology, MESH: Phenotype, Microbiology, Food-poisoning, 03 medical and health sciences, medicine, Pulsed-field gel electrophoresis, Humans, MESH: Food Microbiology, 030304 developmental biology, MESH: Humans, Base Sequence, 030306 microbiology, Outbreak, MESH: Food Contamination, MESH: Cluster Analysis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: France, Food Microbiology, Food Science
Abstract

International audience; Enterotoxins produced by Staphylococcus aureus are responsible for staphylococcal food-poisoning outbreaks (SFPO). In France, SFPO are the second cause of food-borne diseases after Salmonella. However, very little is known about the strains involved. The objective of this study was to characterize the staphylococcal strains related to these SFPO through phenotypic and genotypic analyses. A total of 178 coagulase-positive staphylococcal isolates recovered from 31 SFPO (1981-2002) were screened through biotyping. Thirty-three strains representative of the different biotypes in each SFPO were further examined for SmaI macrorestriction-type, phage-type, resistance to various antimicrobial drugs, presence of staphylococcal enterotoxin (se) genes sea to sei, and production of enterotoxins SEA to SED. All these 33 strains were identified as S. aureus species: 27 were of human biotypes and six ovine or non-host-specific biotypes. Most (74.1%) strains reacted with group III phages. Eleven strains were resistant to at least two classes of antibiotics and among them, two were resistant to methicillin. Twenty-nine strains carried one or several of the eight se genes tested; the gene sea was most common (n=23), and often linked to sed (n=12) or seh (n=5). The novel se genes seg-i were in all cases associated with se genes sea to sed except for one strain which carried only seg and sei. Pulsed-Field Gel Electrophoresis (PFGE) of SmaI macrorestriction digests of the 33 strains discriminated 32 PFGE patterns grouped into nine biotype-specific clusters. All five strains carrying sea and seh were grouped together into the same sub-cluster. Three of the four se-gene-negative strains were in one PFGE cluster: all four should be tested for se genes not included in this study and, if negative, be further investigated for the presence of unidentified SEs.

Published
2007

12. Shigella flexneri 2a strain 2457T expresses three members of the H-NS-like protein family: characterization of the Sfh protein

Author

Christophe Beloin, Padraig Deighan, Charles J. Dorman, Marie Doyle, Génétique des Biofilms, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of Dublin, This work was supported by European Training and Mobility of Researchers Award ERBFMRXCT98-0164, Wellcome Trust Award 064284/Z01/Z and Enterprise Ireland Award SC/2002/22. P. Deighan was supported by a Wellcome Trust Prize Fellowship. The research described in this paper was performed in compliance with current laws governing genetic experimentation in the Republic of Ireland, We thank Philippe Bertin for the E. coli strains BE1414 and YK3421, Maria Mavris for S. flexneri strains, and Pablo Garcia Bravo and Antonio Cerqueira for help with protein purification., and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Operon, MESH: Shigella flexneri, Protein family, [SDV]Life Sciences [q-bio], Virulence, Plasmid R27, Shigella flexneri, H-NS protein, 03 medical and health sciences, Plasmid, Bacterial Proteins, MESH: Plasmids, Operon, Genetics, Escherichia coli, MESH: Phylogeny, MESH: Bacterial Proteins, Molecular Biology, Gene, Phylogeny, 030304 developmental biology, Regulator gene, Regulation of gene expression, MESH: Gene Expression Regulation, Bacterial, 0303 health sciences, biology, MESH: Escherichia coli, 030306 microbiology, Structural gene, Sfh protein, General Medicine, Gene Expression Regulation, Bacterial, biology.organism_classification, Molecular biology, DNA-Binding Proteins, StpA protein, MESH: DNA-Binding Proteins, Plasmids
Abstract

Shigella flexneri 2a is known to express the H-NS nucleoid-structuring protein and the paralogous protein StpA. Using bioinformatic analysis we have now discovered a third member of the H-NS protein family, Sfh (S higella f lexneri H-NS-like protein), in strain 2457T. This protein is encoded by the sfh gene, which is located on a high-molecular-mass plasmid that is closely related to the self-transmissible plasmid R27. When expressed in Escherichia coli, the Sfh protein can complement an hns null mutation, restoring wild-type Bgl, porin protein, and mucoidy phenotypes, and wild-type expression of the fliC and proU genes. While a knockout mutation in the sfh gene alone had no effect on the expression of virulence genes in S. flexneri, an additive effect on virulence gene derepression was seen when the sfh lesion was combined with a mutation in hns. Over-expression of the sfh gene repressed expression of the VirB virulence regulatory protein and transcription of a VirB-dependent structural gene promoter. The purified Sfh protein bound specifically to DNA sequences containing the promoters of the virF and virB virulence regulatory genes. These findings show that Sfh has the ability to influence genetic events beyond the genetic element that encodes it, including the expression of the S. flexneri virulence genes. They raise the possibility of a triangular relationship among three closely related proteins with broad consequences for genetic events in the bacterium that harbours them.

Published
2003