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genomics (72) 72
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1. Full Text Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
by Ohm, R.A and Feau, N and Henrissat, B and Schoch, C.L and Horwitz, B.A and Barry, K.W and Condon, B.J and Copeland, A.C and Dhillon, B and Glaser, F and Hesse, C.N and Kosti, I and LaButti, K and Lindquist, E.A and Lucas, S and Salamov, A.A and Bradshaw, R.E and Ciuffetti, L and Hamelin, R.C and Kema, G.H.J and Lawrence, C and Scott, J.A and Spatafora, J.W and Turgeon, B.G and Wit, de, P.J.G.M and Zhong, S and Goodwin, S.B and Grigoriev, I.V and Joint Genome Institute (JGI)
PLoS Pathogens, ISSN 1553-7366, 2012, Volume 8, Issue 12, p. e1003037
The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad... 
NONRIBOSOMAL PEPTIDE SYNTHETASES | POLYKETIDE SYNTHASE | MICROBIOLOGY | VIRULENCE | MAMMALIAN GENOMES | PROTEIN TOPOLOGY | EVOLUTION | VIROLOGY | BIOSYNTHESIS | SEQUENCE | FUSARIUM-GRAMINEARUM | PARASITOLOGY | INSIGHTS | Point Mutation | Ascomycota - pathogenicity | DNA Transposable Elements - physiology | Chromosomes, Fungal - genetics | Chromosomes, Fungal - metabolism | Ascomycota - genetics | Oxidative Stress - genetics | Plant Diseases - genetics | Plant Diseases - microbiology | Ascomycota - metabolism | Evolution, Molecular | Genes, Fungal - physiology | Fungi, Pathogenic | Microbial genetics | Plant defenses | Genomics | Physiological aspects | Host-parasite relationships | Genetic aspects | Research | Health aspects | Microbiology | Pathogenesis | Taxonomy | Genes | Phylogenetics | Evolution | Lifestyles | Genomes | Metabolism | Chromosomes | cochliobolus-heterostrophus | stagonospora-nodorum | ascomycete leptosphaeria-maculans | phylogenetic trees | polyketide synthase | colletotrichum-graminicola | neurospora-crassa | induced point mutations | fusarium-graminearum | nonribosomal peptide synthetases
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2. Full Text Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis
by Elena Fernandez-Fueyo and Francisco J. Ruiz-Dueñas and Patricia Ferreira and Dimitrios Floudas and David S. Hibbett and Paulo Canessa and Luis F. Larrondo and Tim Y. James and Daniela Seelenfreund and Sergio Lobos and Rubén Polanco and Mario Tello and Yoichi Honda and Takahito Watanabe and Takashi Watanabe and Ryu Jae San and Christian P. Kubicek and Monika Schmoll and Jill Gaskell and Kenneth E. Hammel and Franz J. St. John and Amber Vanden Wymelenberg and Grzegorz Sabat and Sandra Splinter BonDurant and Khajamohiddin Syed and Jagjit S. Yadav and Harshavardhan Doddapaneni and Venkataramanan Subramanian and José L. Lavín and José A. Oguiza and Gumer Perez and Antonio G. Pisabarro and Lucia Ramirez and Francisco Santoyo and Emma Master and Pedro M. Coutinho and Bernard Henrissat and Vincent Lombard and Jon Karl Magnuson and Ursula Kües and Chiaki Hori and Kiyohiko Igarashi and Masahiro Samejima and Benjamin W. Held and Kerrie W. Barry and Kurt M. LaButti and Alla Lapidus and Erika A. Lindquist and Susan M. Lucas and Robert Riley and Asaf A. Salamov and Dirk Hoffmeister and Daniel Schwenk and Yitzhak Hadar and Oded Yarden and Ronald P. de Vries and Ad Wiebenga and Jan Stenlid and Daniel Eastwood and Igor V. Grigoriev and Randy M. Berka and Robert A. Blanchette and Phil Kersten and Angel T. Martinez and Rafael Vicuna and Dan Cullen and Sveriges lantbruksuniversitet
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 4/2012, Volume 109, Issue 14, pp. 5458 - 5463
Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium... 
Fungi | Lignin | Enzymes | Phanerochaete | Genes | Chrysosporium | Genomes | Oxidation | Coriolaceae | Basidiomycota | BASIDIOMYCETE | OXIDATION | HEME PEROXIDASES | FUNGUS | ENZYME | MULTIDISCIPLINARY SCIENCES | SEQUENCE | GENES | LACCASE | EXPRESSION | VERSATILE PEROXIDASE | Hydrolysis | Lignin - metabolism | Oxidation-Reduction | Species Specificity | Basidiomycota - classification | Genomics | Basidiomycota - genetics | Molecular Sequence Data | Phylogeny | Physiological aspects | Fungi, Pathogenic | Genetic aspects | Research | Biological Sciences | Biokemi och molekylärbiologi | Biochemistry and Molecular Biology
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3. Full Text Obligate biotrophy features unraveled by the genomic analysis of rust fungi
by Sébastien Duplessis and Christina A. Cuomo and Yao-Cheng Lin and Andrea Aerts and Emilie Tisserant and Claire Veneault-Fourrey and David L. Joly and Stéphane Hacquard and Joëlle Amselem and Brandi L. Cantarel and Readman Chiu and Pedro M. Coutinho and Nicolas Feau and Matthew Field and Pascal Frey and Eric Gelhaye and Jonathan Goldberg and Manfred G. Grabherr and Chinnappa D. Kodira and Annegret Kohler and Ursula Kües and Erika A. Lindquist and Susan M. Lucas and Rohit Mago and Evan Mauceli and Emmanuelle Morin and Claude Murat and Jasmyn L. Pangilinan and Robert Park and Matthew Pearson and Hadi Quesneville and Nicolas Rouhier and Sharadha Sakthikumar and Asaf A. Salamov and Jeremy Schmutz and Benjamin Selles and Harris Shapiro and Philippe Tanguay and Gerald A. Tuskan and Bernard Henrissat and Yves Van de Peer and Pierre Rouzé and Jeffrey G. Ellis and Peter N. Dodds and Jacqueline E. Schein and Shaobin Zhong and Richard C. Hamelin and Igor V. Grigoriev and Les J. Szabo and Francis Martin
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 5/2011, Volume 108, Issue 22, pp. 9166 - 9171
Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and... 
Datasets | Fungi | Proteins | Pathogens | Enzymes | Rust fungi | Genes | Genomes | Plants | Parasite hosts | Comparative genomics | Basidiomycete | Evolution | Rust disease | Plant pathogen | basidiomycete | plant pathogen | SEQUENCES | MULTIDISCIPLINARY SCIENCES | rust disease | HOST | evolution | SMUT FUNGI | comparative genomics | POPLAR | RESISTANCE | HAUSTORIA | SYMBIOSIS | INSIGHTS | Oligonucleotide Array Sequence Analysis | Plant Diseases - microbiology | Gene Expression Profiling | Phylogeny | Fungi - genetics | Sequence Analysis, DNA | Nitrates - chemistry | Genome, Fungal | Sulfates - chemistry | Basidiomycota - genetics | Genes, Fungal | Models, Genetic | Genome | Triticum - microbiology | Plant Leaves - microbiology | Genomics | Physiological aspects | Genetic aspects | Research | Life Sciences | Agricultural sciences | Biological Sciences
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4. Full Text Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche
by Emmanuelle Morin and Annegret Kohler and Adam R. Baker and Marie Foulongne-Oriol and Vincent Lombard and Laszlo G. Nagy and Robin A. Ohm and Aleksandrina Patyshakuliyeva and Annick Brun and Andrea L. Aerts and Andrew M. Bailey and Christophe Billette and Pedro M. Coutinho and Greg Deakin and Harshavardhan Doddapaneni and Dimitrios Floudas and Jane Grimwood and Kristiina Hildén and Ursula Kües and Kurt M. LaButti and Alla Lapidus and Erika A. Lindquist and Susan M. Lucas and Claude Murat and Robert W. Riley and Asaf A. Salamov and Jeremy Schmutz and Venkataramanan Subramanian and Han A. B. Wösten and Jianping Xu and Daniel C. Eastwood and Gary D. Foster and Anton S. M. Sonnenberg and Dan Cullen and Ronald P. de Vries and Taina Lundell and David S. Hibbett and Bernard Henrissat and Kerry S. Burton and Richard W. Kerrigan and Michael P. Challen and Igor V. Grigoriev and Francis Martin
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 10/2012, Volume 109, Issue 43, pp. 17501 - 17506
Agaricus bisporus is the model fungus for the adaptation, persistence, growth in the humic-rich leaf-litter environment. Aside from its role, A. bisporus has... 
Fungi | Compost | Enzymes | Lignin | Fruiting bodies | Agaricus | Mushrooms | Genes | Genomes | Mycelium | Litter decay | Wood decay fungi | Humic substances | Carbohydrate-active enzymes | FUNGI | MULTIDISCIPLINARY SCIENCES | DECOMPOSITION | humic substances | SUBSTANCES | carbohydrate-active enzymes | CHROMOSOMES | CULTIVATED MUSHROOM | wood decay fungi | COPRINUS-CINEREUS | COPRINOPSIS-CINEREA | GENE | litter decay | SCHIZOPHYLLUM-COMMUNE | DEGRADATION | Agaricus - genetics | Agaricus - metabolism | Lignin - metabolism | Genome, Fungal | Adaptation, Physiological - genetics | Ecology | Agaricus - physiology | Evolution, Molecular | Physiological aspects | Genetic aspects | Research | Niche (Ecology) | Genomics | Life Sciences | Biological Sciences | cultivated mushroom | substances | fungi | gene | coprinus-cinereus | chromosomes | schizophyllum-commune | decomposition | degradation | coprinopsis-cinerea
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5. Full Text Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
by Robert Riley and Asaf A. Salamov and Daren W. Brown and Laszlo G. Nagy and Dimitrios Floudas and Benjamin W. Held and Anthony Levasseur and Vincent Lombard and Emmanuelle Morin and Robert Otillar and Erika A. Lindquist and Hui Sun and Kurt M. LaButti and Jeremy Schmutz and Dina Jabbour and Hong Luoi and Scott E. Baker and Antonio G. Pisabarro and Jonathan D. Walton and Robert A. Blanchette and Bernard Henrissat and Francis Martin and Dan Cullen and David S. Hibbett and Igor V. Grigoriev and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States) and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 7/2014, Volume 111, Issue 27, pp. 9923 - 9928
Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts.... 
Fungi | Oxidases | Enzymes | Lignin | Phanerochaete | Brown rot fungi | Phylogenetics | Genomes | Basidiomycota | White rot fungi | Lignocellulose | Bioenergy | Phylogenomics | hylogenomics | DEGRADING ENZYMES | LIGNIN PEROXIDASE | MOLECULAR-BIOLOGY | SECONDARY METABOLISM | MULTIDISCIPLINARY SCIENCES | bioenergy | HETEROBASIDION-ANNOSUM | SERPULA-LACRYMANS | PHANEROCHAETE-CHRYSOSPORIUM | GLOEOPHYLLUM-TRABEUM | SCHIZOPHYLLUM-COMMUNE | POSTIA-PLACENTA | lignocellulose | Lignin - metabolism | Genome, Fungal | Wood | Basidiomycota - classification | Basidiomycota - genetics | Molecular Sequence Data | Phylogeny | Basidiomycota - metabolism | Microbiological research | Mycology | Genomics | Distribution | Genetic research | Genetic aspects | Research | Identification and classification | Life Sciences | ENVIRONMENTAL SCIENCES | BASIC BIOLOGICAL SCIENCES | phylogenomics | Biological Sciences
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6. Full Text The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
by Dimitrios Flundas and Manfred Binder and Robert Riley and Kerrie Barry and Robert A. Blanchette and Bernard Henrissat and Angel T. Martínez and Robert Otillar and Joseph W. Spatafora and Jagjit S. Yadav and Andrea Aerts and Isabelle Benoit and Alex Boyd and Alexis Carlson and Alex Copeland and Pedro M. Coutinho and Ronald P. de Vries and Patricia Ferreira and Keisha Findley and Brian Foster and Jill Gaskell and Dylan Glotzer and Paweł Górecki and Joseph Heitman and Cedar Hesse and Chiaki Hori and Kiyohiko Igarashi and Joel A. Jurgens and Nathan Kallen and Phil Kersten and Annegret Kohler and Ursula Kües and T. K. Arun Kumar and Alan Kuo and Kurt LaButti and Luis F. Larrondo and Erika Lindquist and Albee Ling and Vincent Lombard and Susan Lucas and Taina Lundell and Rachael Martin and David J. McLaughlin and Ingo Morgenstern and Emanuelle Morin and Claude Murat and Laszlo G. Nagy and Matt Nolan and Robin A. Ohm and Aleksandrina Patyshakuliyeva and Antonis Rokas and Francisco J. Ruiz-Dueñas and Grzegorz Sabat and Asaf Salamov and Masahiro Samejima and Jeremy Schmutz and Jason C. Slot and Franz St. John and Jan Stenlid and Hui Sun and Sheng Sun and Khajamohiddin Syed and Adrian Tsang and Ad Wiebenga and Darcy Young and Antonio Pisabarro and Daniel C. Eastwood and Francis Martin and Dan Cullen and Igor V. Grigoriev and David S. Hibbett and Joint Genome Institute (JGI) and Sveriges lantbruksuniversitet
Science, ISSN 0036-8075, 6/2012, Volume 336, Issue 6089, pp. 1715 - 1719
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 | Biological taxonomies | Enzymes | Mycology | REPORTS | Chrysosporium | Evolution | Genomes | Fungal genomes | Phylogeny | Bioinformatics | PHANEROCHAETE-CHRYSOSPORIUM | EVOLUTION | GENE | MODELS | WOOD DECAY | MULTIDISCIPLINARY SCIENCES | SEQUENCE | DEGRADATION | CELLULOSE | PEROXIDASES | FAMILY | Lignin - metabolism | Genome, Fungal | Basidiomycota - enzymology | Basidiomycota - classification | Bayes Theorem | Basidiomycota - genetics | Peroxidases - metabolism | Indoles | Peroxidases - genetics | Wood - metabolism | Evolution, Molecular | Fungi | Biodegradation | Physiological aspects | Genetic aspects | Research | Genes | Decomposition | Sampling | Dating | Life Sciences | Structural Biology | Strukturbiologi | Evolutionsbiologi | Ecology | Bioinformatik och systembiologi | Evolutionary Biology | Ekologi | Bioinformatics and Systems Biology
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7. Full Text The Sorghum bicolor genome and the diversification of grasses
by Paterson, Andrew H and Bowers, John E and Bruggmann, Rémy and Dubchak, Inna and Grimwood, Jane and Gundlach, Heidrun and Haberer, Georg and Hellsten, Uffe and Mitros, Therese and Poliakov, Alexander and Schmutz, Jeremy and Spannagl, Manuel and Tang, Haibao and Wang, Xiyin and Wicker, Thomas and Bharti, Arvind K and Chapman, Jarrod and Feltus, F. Alex and Gowik, Udo and Grigoriev, Igor V and Lyons, Eric and Maher, Christopher A and Martis, Mihaela and Narechania, Apurva and Otillar, Robert P and Penning, Bryan W and Salamov, Asaf A and Wang, Yu and Zhang, Lifang and Carpita, Nicholas C and Freeling, Michael and Gingle, Alan R and Hash, C. Thomas and Keller, Beat and Klein, Patricia and Kresovich, Stephen and McCann, Maureen C and Ming, Ray and Peterson, Daniel G and Mehboob-Ur-Rahman, Mehboob-Ur-Rahman and Ware, Doreen and Westhoff, Peter and Mayer, Klaus F. X and Messing, Joachim and Rokhsar, Daniel S and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 01/2009, Volume 457, Issue 7229, pp. 551 - 556
Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the similar to 730-... 
RECOMBINATION | RICE GENOME | EVOLUTION | MAIZE GENOME | MULTIDISCIPLINARY SCIENCES | WIDE ANALYSIS | SEQUENCE | GENES | DUPLICATION | IDENTIFICATION | CELL-WALLS | Gene Duplication | Zea mays - genetics | Genome, Plant - genetics | Genes, Plant | Poaceae - genetics | Populus - genetics | Sequence Analysis, DNA | Arabidopsis - genetics | Sequence Alignment | Oryza - genetics | Recombination, Genetic - genetics | Sorghum - genetics | Chromosomes, Plant - genetics | Evolution, Molecular | Sequence Deletion - genetics | Evaluation | Genomics | Physiological aspects | Sorghum | Genetic aspects | Grasses | Research | Biological diversity | Genetics | Drought | Genes
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8. Full Text The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex
by Guillaume Blanc and Garry Duncan and Irina Agarkova and Mark Borodovsky and James Gurnon and Alan Kuo and Erika Lindquist and Susan Lucas and Jasmyn Pangilinan and Juergen Polle and Asaf Salamov and Astrid Terry and Takashi Yamada and David D. Dunigan and Igor V. Grigoriev and Jean-Michel Claverie and James L. Van Etten and Joint Genome Institute (JGI)
The Plant Cell, ISSN 1040-4651, 9/2010, Volume 22, Issue 9, pp. 2943 - 2955
Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model... 
Enzymes | Cell walls | Algae | Viruses | Evolution | Green algae | Genomes | Chitin | Plants | Flagella | PHYLOGENY | CHLOROVIRUS | BIOCHEMISTRY & MOLECULAR BIOLOGY | LAND | IDENTIFICATION | PLANT SCIENCES | CELL BIOLOGY | AUXIN | CELL-WALL | GENUS CHLORELLA | EVOLUTION | GENES | INSIGHTS | Symbiosis | Chlorella - virology | Multigene Family | Molecular Sequence Data | Genome, Plant | Sequence Analysis, DNA | Chlorella - genetics | Reproduction | Base Composition | Cell Wall - metabolism | Plant Growth Regulators - genetics | Repetitive Sequences, Nucleic Acid | Flagella - genetics | DNA, Plant - genetics | Evolution, Molecular | Expressed Sequence Tags
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9. Full Text Ab initio gene finding in Drosophila genomic DNA
by Salamov, Asaf A and Solovyev, Victor V
Genome Research, ISSN 1088-9051, 04/2000, Volume 10, Issue 4, pp. 516 - 522
Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained using Fgenes (human gene predictor) and Fgenesh programs that... 
PROTEIN | MESSENGER-RNA | DATABASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMISTRY & MOLECULAR BIOLOGY | SEQUENCE | GENETICS & HEREDITY | SIMILARITY | MELANOGASTER | PREDICTION
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10. Full Text The amphioxus genome and the evolution of the chordate karyotype
by Putnam, Nicholas H and Butts, Thomas and Ferrier, David E. K and Furlong, Rebecca F and Hellsten, Uffe and Kawashima, Takeshi and Robinson-Rechavi, Marc and Shoguchi, Eiichi and Terry, Astrid and Yu Jr, Kai and Benito-Gutiérrez, Èlia and Dubchak, Inna and Garcia-Fernàndez, Jordi and Gibson-Brown, Jeremy J and Grigoriev, Igor V and Horton, Amy C and De Jong, Pieter J and Jurka, Jerzy and Kapitonov, Vladimir V and Kohara, Yuji and Kuroki, Yoko and Lindquist, Erika and Lucas, Susan and Osoegawa, Kazutoyo and Pennacchio, Len A and Salamov, Asaf A and Satou, Yutaka and Sauka-Spengler, Tatjana and Schmutz, Jeremy and Shin-I, Tadasu and Toyoda, Atsushi and Bronner-Fraser, Marianne and Fujiyama, Asao and Holland, Linda Z and Holland, Peter W. H and Satoh, Nori and Rokhsar, Daniel S and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 06/2008, Volume 453, Issue 7198, pp. 1064 - 1071
Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the... 
NERVOUS-SYSTEM | ORIGINS | ANCESTRAL VERTEBRATE | RECONSTRUCTION | MULTIDISCIPLINARY SCIENCES | GENE DUPLICATIONS | TELEOST FISH | CHROMOSOMES | CIONA-INTESTINALIS | REVEALS | INSIGHTS | Chordata - genetics | Gene Duplication | Multigene Family | Introns - genetics | Vertebrates - genetics | Humans | Genome - genetics | Synteny | Genes - genetics | Phylogeny | Proteins - genetics | Animals | Vertebrates - classification | Time Factors | Karyotyping | DNA Transposable Elements - genetics | Conserved Sequence | Polymorphism, Genetic - genetics | Chordata - classification | Evolution, Molecular | Genetic Linkage | Karyotypes | Evaluation | Genomes | Genetic variation | Identification and classification | Studies | Vertebrates | Endocrine system | Genomics | Genes | Genetics | Evolution | Comparative analysis | Chromosomes
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