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  • 1
    Publication Date: 2012-06-30
    Description: Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Floudas, Dimitrios -- Binder, Manfred -- Riley, Robert -- Barry, Kerrie -- Blanchette, Robert A -- Henrissat, Bernard -- Martinez, Angel T -- Otillar, Robert -- Spatafora, Joseph W -- Yadav, Jagjit S -- Aerts, Andrea -- Benoit, Isabelle -- Boyd, Alex -- Carlson, Alexis -- Copeland, Alex -- Coutinho, Pedro M -- de Vries, Ronald P -- Ferreira, Patricia -- Findley, Keisha -- Foster, Brian -- Gaskell, Jill -- Glotzer, Dylan -- Gorecki, Pawel -- Heitman, Joseph -- Hesse, Cedar -- Hori, Chiaki -- Igarashi, Kiyohiko -- Jurgens, Joel A -- Kallen, Nathan -- Kersten, Phil -- Kohler, Annegret -- Kues, Ursula -- Kumar, T K Arun -- Kuo, Alan -- LaButti, Kurt -- Larrondo, Luis F -- Lindquist, Erika -- Ling, Albee -- Lombard, Vincent -- Lucas, Susan -- Lundell, Taina -- Martin, Rachael -- McLaughlin, David J -- Morgenstern, Ingo -- Morin, Emanuelle -- Murat, Claude -- Nagy, Laszlo G -- Nolan, Matt -- Ohm, Robin A -- Patyshakuliyeva, Aleksandrina -- Rokas, Antonis -- Ruiz-Duenas, Francisco J -- Sabat, Grzegorz -- Salamov, Asaf -- Samejima, Masahiro -- Schmutz, Jeremy -- Slot, Jason C -- St John, Franz -- Stenlid, Jan -- Sun, Hui -- Sun, Sheng -- Syed, Khajamohiddin -- Tsang, Adrian -- Wiebenga, Ad -- Young, Darcy -- Pisabarro, Antonio -- Eastwood, Daniel C -- Martin, Francis -- Cullen, Dan -- Grigoriev, Igor V -- Hibbett, David S -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1715-9. doi: 10.1126/science.1221748.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Clark University, Worcester, MA 01610, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745431" target="_blank"〉PubMed〈/a〉
    Keywords: Basidiomycota/classification/*enzymology/*genetics ; Bayes Theorem ; *Evolution, Molecular ; *Genome, Fungal ; Indoles ; Lignin/*metabolism ; Peroxidases/*genetics/metabolism ; Wood/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-06-12
    Description: 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〉
    Keywords: Eucalyptus/classification/*genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Plant ; Inbreeding ; Phylogeny
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2011-04-23
    Description: The fission yeast clade--comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus--occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131103/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131103/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rhind, Nicholas -- Chen, Zehua -- Yassour, Moran -- Thompson, Dawn A -- Haas, Brian J -- Habib, Naomi -- Wapinski, Ilan -- Roy, Sushmita -- Lin, Michael F -- Heiman, David I -- Young, Sarah K -- Furuya, Kanji -- Guo, Yabin -- Pidoux, Alison -- Chen, Huei Mei -- Robbertse, Barbara -- Goldberg, Jonathan M -- Aoki, Keita -- Bayne, Elizabeth H -- Berlin, Aaron M -- Desjardins, Christopher A -- Dobbs, Edward -- Dukaj, Livio -- Fan, Lin -- FitzGerald, Michael G -- French, Courtney -- Gujja, Sharvari -- Hansen, Klavs -- Keifenheim, Dan -- Levin, Joshua Z -- Mosher, Rebecca A -- Muller, Carolin A -- Pfiffner, Jenna -- Priest, Margaret -- Russ, Carsten -- Smialowska, Agata -- Swoboda, Peter -- Sykes, Sean M -- Vaughn, Matthew -- Vengrova, Sonya -- Yoder, Ryan -- Zeng, Qiandong -- Allshire, Robin -- Baulcombe, David -- Birren, Bruce W -- Brown, William -- Ekwall, Karl -- Kellis, Manolis -- Leatherwood, Janet -- Levin, Henry -- Margalit, Hanah -- Martienssen, Rob -- Nieduszynski, Conrad A -- Spatafora, Joseph W -- Friedman, Nir -- Dalgaard, Jacob Z -- Baumann, Peter -- Niki, Hironori -- Regev, Aviv -- Nusbaum, Chad -- BB/E023754/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- DP1 OD003958/OD/NIH HHS/ -- R01 GM069957/GM/NIGMS NIH HHS/ -- R01 GM076396/GM/NIGMS NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-06/HG/NHGRI NIH HHS/ -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 May 20;332(6032):930-6. doi: 10.1126/science.1203357. Epub 2011 Apr 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA. nick.rhind@umassmed.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21511999" target="_blank"〉PubMed〈/a〉
    Keywords: Centromere/genetics/physiology/ultrastructure ; DNA Transposable Elements ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Genes, Mating Type, Fungal ; *Genome, Fungal ; Genomics ; Glucose/metabolism ; Meiosis ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; RNA, Antisense/genetics ; RNA, Fungal/genetics ; RNA, Small Interfering/genetics ; RNA, Untranslated/genetics ; Regulatory Elements, Transcriptional ; Schizosaccharomyces/*genetics/growth & development/metabolism ; Schizosaccharomyces pombe Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Species Specificity ; Transcription Factors/genetics/metabolism ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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