ALBERT

Beschreibung: 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Myburg, Alexander A -- Grattapaglia, Dario -- Tuskan, Gerald A -- Hellsten, Uffe -- Hayes, Richard D -- Grimwood, Jane -- Jenkins, Jerry -- Lindquist, Erika -- Tice, Hope -- Bauer, Diane -- Goodstein, David M -- Dubchak, Inna -- Poliakov, Alexandre -- Mizrachi, Eshchar -- Kullan, Anand R K -- Hussey, Steven G -- Pinard, Desre -- van der Merwe, Karen -- Singh, Pooja -- van Jaarsveld, Ida -- Silva-Junior, Orzenil B -- Togawa, Roberto C -- Pappas, Marilia R -- Faria, Danielle A -- Sansaloni, Carolina P -- Petroli, Cesar D -- Yang, Xiaohan -- Ranjan, Priya -- Tschaplinski, Timothy J -- Ye, Chu-Yu -- Li, Ting -- Sterck, Lieven -- Vanneste, Kevin -- Murat, Florent -- Soler, Marcal -- Clemente, Helene San -- Saidi, Naijib -- Cassan-Wang, Hua -- Dunand, Christophe -- Hefer, Charles A -- Bornberg-Bauer, Erich -- Kersting, Anna R -- Vining, Kelly -- Amarasinghe, Vindhya -- Ranik, Martin -- Naithani, Sushma -- Elser, Justin -- Boyd, Alexander E -- Liston, Aaron -- Spatafora, Joseph W -- Dharmwardhana, Palitha -- Raja, Rajani -- Sullivan, Christopher -- Romanel, Elisson -- Alves-Ferreira, Marcio -- Kulheim, Carsten -- Foley, William -- Carocha, Victor -- Paiva, Jorge -- Kudrna, David -- Brommonschenkel, Sergio H -- Pasquali, Giancarlo -- Byrne, Margaret -- Rigault, Philippe -- Tibbits, Josquin -- Spokevicius, Antanas -- Jones, Rebecca C -- Steane, Dorothy A -- Vaillancourt, Rene E -- Potts, Brad M -- Joubert, Fourie -- Barry, Kerrie -- Pappas, Georgios J -- Strauss, Steven H -- Jaiswal, Pankaj -- Grima-Pettenati, Jacqueline -- Salse, Jerome -- Van de Peer, Yves -- Rokhsar, Daniel S -- Schmutz, Jeremy -- England -- Nature. 2014 Jun 19;510(7505):356-62. doi: 10.1038/nature13308. Epub 2014 Jun 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa. ; 1] Laboratorio de Genetica Vegetal, EMBRAPA Recursos Geneticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasilia, Brazil [2] Programa de Ciencias Genomicas e Biotecnologia - Universidade Catolica de Brasilia SGAN 916, 70790-160 Brasilia, Brazil. ; 1] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. ; US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA. ; HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USA. ; Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Private bag X20, Pretoria 0028, South Africa. ; Laboratorio de Bioinformatica, EMBRAPA Recursos Geneticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasilia, Brazil. ; Laboratorio de Genetica Vegetal, EMBRAPA Recursos Geneticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasilia, Brazil. ; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. ; Department of Plant Biotechnology and Bioinformatics (VIB), Ghent University, Technologiepark 927, B-9000 Ghent, Belgium. ; INRA/UBP UMR 1095, 5 Avenue de Beaulieu, 63100 Clermont Ferrand, France. ; Laboratoire de Recherche en Sciences Vegetales, UMR 5546, Universite Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France. ; 1] Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver V6T 1Z4, Canada. ; Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Muenster, Huefferstrasse 1, D-48149, Muenster, Germany. ; 1] Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Muenster, Huefferstrasse 1, D-48149, Muenster, Germany [2] Department of Bioinformatics, Institute for Computer Science, University of Duesseldorf, Universitatsstrasse 1, 40225 Dusseldorf, Germany. ; Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon 97331, USA. ; 1] Department of Botany and Plant Pathology, Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA [2] Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA. ; Department of Botany and Plant Pathology, Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA. ; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA. ; 1] Laboratorio de Biologia Evolutiva Teorica e Aplicada, Departamento de Genetica, Universidade Federal do Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Paulo Rocco, 21949900 Rio de Janeiro, Brazil [2] Departamento de Biotecnologia, Escola de Engenharia de Lorena-Universidade de Sao Paulo (EEL-USP), CP116, 12602-810, Lorena-SP, Brazil [3] Laboratorio de Genetica Molecular Vegetal (LGMV), Departamento de Genetica, Universidade Federal do Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Paulo Rocco, 21949900 Rio de Janeiro, Brazil. ; Laboratorio de Genetica Molecular Vegetal (LGMV), Departamento de Genetica, Universidade Federal do Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Paulo Rocco, 21949900 Rio de Janeiro, Brazil. ; Research School of Biology, Australian National University, Canberra 0200, Australia. ; 1] Laboratoire de Recherche en Sciences Vegetales, UMR 5546, Universite Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France [2] IICT/MNE; Palacio Burnay - Rua da Junqueira, 30, 1349-007 Lisboa, Portugal [3] IBET/ITQB, Av. Republica, Quinta do Marques, 2781-901 Oeiras, Portugal. ; 1] IICT/MNE; Palacio Burnay - Rua da Junqueira, 30, 1349-007 Lisboa, Portugal [2] IBET/ITQB, Av. Republica, Quinta do Marques, 2781-901 Oeiras, Portugal. ; Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA. ; Dep. de Fitopatologia, Universidade Federal de Vicosa, Vicosa 36570-000, Brazil. ; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, Brazil. ; Science and Conservation Division, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, Western Australia 6983, Australia. ; GYDLE, 1363 av. Maguire, suite 301, Quebec, Quebec G1T 1Z2, Canada. ; Department of Environment and Primary Industries, Victorian Government, Melbourne, Victoria 3085, Australia. ; Melbourne School of Land and Environment, University of Melbourne, Melbourne, Victoria 3010, Australia. ; School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia. ; 1] School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia [2] Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland 4558, Australia. ; 1] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Private bag X20, Pretoria 0028, South Africa. ; Departamento de Biologia Celular, Universidade de Brasilia, Brasilia 70910-900, Brazil. ; 1] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Department of Plant Biotechnology and Bioinformatics (VIB), Ghent University, Technologiepark 927, B-9000 Ghent, Belgium. ; 1] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24919147" target="_blank"〉PubMed〈/a〉

Beschreibung: Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the 〉100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (〉10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nystedt, Bjorn -- Street, Nathaniel R -- Wetterbom, Anna -- Zuccolo, Andrea -- Lin, Yao-Cheng -- Scofield, Douglas G -- Vezzi, Francesco -- Delhomme, Nicolas -- Giacomello, Stefania -- Alexeyenko, Andrey -- Vicedomini, Riccardo -- Sahlin, Kristoffer -- Sherwood, Ellen -- Elfstrand, Malin -- Gramzow, Lydia -- Holmberg, Kristina -- Hallman, Jimmie -- Keech, Olivier -- Klasson, Lisa -- Koriabine, Maxim -- Kucukoglu, Melis -- Kaller, Max -- Luthman, Johannes -- Lysholm, Fredrik -- Niittyla, Totte -- Olson, Ake -- Rilakovic, Nemanja -- Ritland, Carol -- Rossello, Josep A -- Sena, Juliana -- Svensson, Thomas -- Talavera-Lopez, Carlos -- Theissen, Gunter -- Tuominen, Hannele -- Vanneste, Kevin -- Wu, Zhi-Qiang -- Zhang, Bo -- Zerbe, Philipp -- Arvestad, Lars -- Bhalerao, Rishikesh -- Bohlmann, Joerg -- Bousquet, Jean -- Garcia Gil, Rosario -- Hvidsten, Torgeir R -- de Jong, Pieter -- MacKay, John -- Morgante, Michele -- Ritland, Kermit -- Sundberg, Bjorn -- Thompson, Stacey Lee -- Van de Peer, Yves -- Andersson, Bjorn -- Nilsson, Ove -- Ingvarsson, Par K -- Lundeberg, Joakim -- Jansson, Stefan -- England -- Nature. 2013 May 30;497(7451):579-84. doi: 10.1038/nature12211. Epub 2013 May 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23698360" target="_blank"〉PubMed〈/a〉

Beschreibung: Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Olsen, Jeanine L -- Rouze, Pierre -- Verhelst, Bram -- Lin, Yao-Cheng -- Bayer, Till -- Collen, Jonas -- Dattolo, Emanuela -- De Paoli, Emanuele -- Dittami, Simon -- Maumus, Florian -- Michel, Gurvan -- Kersting, Anna -- Lauritano, Chiara -- Lohaus, Rolf -- Topel, Mats -- Tonon, Thierry -- Vanneste, Kevin -- Amirebrahimi, Mojgan -- Brakel, Janina -- Bostrom, Christoffer -- Chovatia, Mansi -- Grimwood, Jane -- Jenkins, Jerry W -- Jueterbock, Alexander -- Mraz, Amy -- Stam, Wytze T -- Tice, Hope -- Bornberg-Bauer, Erich -- Green, Pamela J -- Pearson, Gareth A -- Procaccini, Gabriele -- Duarte, Carlos M -- Schmutz, Jeremy -- Reusch, Thorsten B H -- Van de Peer, Yves -- England -- Nature. 2016 Feb 18;530(7590):331-5. doi: 10.1038/nature16548. Epub 2016 Jan 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103, 9700 CC Groningen, The Netherlands. ; Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium. ; GEOMAR Helmholtz Centre for Ocean Research-Kiel, Evolutionary Ecology, Dusternbrooker Weg 20, D-24105 Kiel, Germany. ; Sorbonne Universite, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France. ; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy. ; Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Via delle Scienze 206, 33100 Udine, Italy. ; INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France. ; Institute for Evolution and Biodiversity, Westfalische Wilhelms-University of Munster, Hufferstrasse 1, D-48149 Munster, Germany. ; Institute for Computer Science, Heinrich Heine University, D-40255 Duesseldorf, Germany. ; Department of Biological and Environmental Sciences, Bioinformatics Infrastructure for Life Sciences (BILS), University of Gothenburg, Medicinaregatan 18A, 40530 Gothenburg, Sweden. ; Department of Energy Joint Genome Institute, 2800 Mitchell Dr., #100, Walnut Creek, California 94598, USA. ; Environmental and Marine Biology, Faculty of Science and Engineering, Abo Akademi University, Artillerigatan 6, FI-20520 Turku/Abo, Finland. ; HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA. ; Marine Ecology Group, Nord University, Postbox 1490, 8049 Bodo, Norway. ; Amplicon Express, 2345 NE Hopkins Ct., Pullman, Washington 99163, USA. ; School of Marine Science and Policy, Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, 15-Innovation Way, Newark, Delaware 19711, USA. ; Marine Ecology and Evolution, Centre for Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal. ; King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia. ; University of Kiel, Faculty of Mathematics and Natural Sciences, Christian-Albrechts-Platz 4, 24118 Kiel, Germany. ; Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa. ; Bioinformatics Institute Ghent, Ghent University, Ghent B-9000, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26814964" target="_blank"〉PubMed〈/a〉