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1. Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships

Author

Sonia Chadha, Sayaji T. Mehetre, Ravindra Bansal, Alan Kuo, Andrea Aerts, Igor V. Grigoriev, Irina S. Druzhinina, and Prasun K. Mukherjee

Subjects
Biotechnology, TP248.13-248.65
Abstract

Abstract Background Cytochrome P450s form an important group of enzymes involved in xenobiotics degradation and metabolism, both primary and secondary. These enzymes are also useful in industry as biotechnological tools for bioconversion and a few are reported to be involved in pathogenicity. Trichoderma spp. are widely used in industry and agriculture and are known for their biosynthetic potential of a large number of secondary metabolites. For realising the full biosynthetic potential of an organism, it is important to do a genome-wide annotation and cataloguing of these enzymes. Results Here, we have studied the genomes of seven species (T. asperellum, T. atroviride, T. citrinoviride, T. longibrachiatum, T. reesei , T. harzianum and T. virens) and identified a total of 477 cytochrome P450s. We present here the classification, evolution and structure as well as predicted function of these proteins. This study would pave the way for functional characterization of these groups of enzymes and will also help in realization of their full economic potential. Conclusion Our CYPome annotation and evolutionary studies of the seven Trichoderma species now provides opportunities for exploration of research-driven strategies to select Trichoderma species for various applications especially in relation to secondary metabolism and degradation of environmental pollutants.

Published
2018
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2. Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12

Author

Jill Gaskell, Phil Kersten, Luis F. Larrondo, Paulo Canessa, Diego Martinez, David Hibbett, Monika Schmoll, Christian P. Kubicek, Angel T. Martinez, Jagjit Yadav, Emma Master, Jon Karl Magnuson, Debbie Yaver, Randy Berka, Kathleen Lail, Cindy Chen, Kurt LaButti, Matt Nolan, Anna Lipzen, Andrea Aerts, Robert Riley, Kerrie Barry, Bernard Henrissat, Robert Blanchette, Igor V. Grigoriev, and Dan Cullen

Subjects
Postia placenta, Rhodonia placenta, Monokaryon, Genetics, QH426-470
Published
2017
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3. Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts.

Author

Irina S Druzhinina, Komal Chenthamara, Jian Zhang, Lea Atanasova, Dongqing Yang, Youzhi Miao, Mohammad J Rahimi, Marica Grujic, Feng Cai, Shadi Pourmehdi, Kamariah Abu Salim, Carina Pretzer, Alexey G Kopchinskiy, Bernard Henrissat, Alan Kuo, Hope Hundley, Mei Wang, Andrea Aerts, Asaf Salamov, Anna Lipzen, Kurt LaButti, Kerrie Barry, Igor V Grigoriev, Qirong Shen, and Christian P Kubicek

Subjects
Genetics, QH426-470
Abstract

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.

Published
2018
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5. Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control.

Author

Rafael E Arango Isaza, Caucasella Diaz-Trujillo, Braham Dhillon, Andrea Aerts, Jean Carlier, Charles F Crane, Tristan V de Jong, Ineke de Vries, Robert Dietrich, Andrew D Farmer, Claudia Fortes Fereira, Suzana Garcia, Mauricio Guzman, Richard C Hamelin, Erika A Lindquist, Rahim Mehrabi, Olman Quiros, Jeremy Schmutz, Harris Shapiro, Elizabeth Reynolds, Gabriel Scalliet, Manoel Souza, Ioannis Stergiopoulos, Theo A J Van der Lee, Pierre J G M De Wit, Marie-Françoise Zapater, Lute-Harm Zwiers, Igor V Grigoriev, Stephen B Goodwin, and Gert H J Kema

Subjects
Genetics, QH426-470
Abstract

Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus Pseudocercospora fijiensis (previously: Mycosphaerella fijiensis), is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase the economic and environmental costs to produce banana. Weekly applications in most banana plantations lead to rapid evolution of fungicide-resistant strains within populations causing disease-control failures throughout the world. Given its extremely high economic importance, two strains of P. fijiensis were sequenced and assembled with the aid of a new genetic linkage map. The 74-Mb genome of P. fijiensis is massively expanded by LTR retrotransposons, making it the largest genome within the Dothideomycetes. Melting-curve assays suggest that the genomes of two closely related members of the Sigatoka disease complex, P. eumusae and P. musae, also are expanded. Electrophoretic karyotyping and analyses of molecular markers in P. fijiensis field populations showed chromosome-length polymorphisms and high genetic diversity. Genetic differentiation was also detected using neutral markers, suggesting strong selection with limited gene flow at the studied geographic scale. Frequencies of fungicide resistance in fungicide-treated plantations were much higher than those in untreated wild-type P. fijiensis populations. A homologue of the Cladosporium fulvum Avr4 effector, PfAvr4, was identified in the P. fijiensis genome. Infiltration of the purified PfAVR4 protein into leaves of the resistant banana variety Calcutta 4 resulted in a hypersensitive-like response. This result suggests that Calcutta 4 could carry an unknown resistance gene recognizing PfAVR4. Besides adding to our understanding of the overall Dothideomycete genome structures, the P. fijiensis genome will aid in developing fungicide treatment schedules to combat this pathogen and in improving the efficiency of banana breeding programs.

Published
2016
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6. Genome Sequence of the Chestnut Blight Fungus Cryphonectria parasitica EP155: A Fundamental Resource for an Archetypical Invasive Plant Pathogen

Author

Jagjit S. Yadav, Jane Grimwood, Asaf Salamov, Andrea Aerts, Igor V. Grigoriev, Angus L. Dawe, Alice C. L. Churchill, Donald L. Nuss, Michael G. Milgroom, Kerrie Barry, Jo Anne Crouch, Jasmyn Pangilinan, Jeremy Schmutz, Myron L. Smith, and Bradley I. Hillman

Subjects
Transposable element, Genetics, Whole genome sequencing, biology, Shotgun sequencing, fungi, Plant Science, biology.organism_classification, Genome, Chestnut blight, Mycovirus, Cryphonectria, Agronomy and Crop Science, Gene
Abstract

Cryphonectria parasitica is the causal agent of chestnut blight, a fungal disease that almost entirely eliminated mature American chestnut from North America over a 50-year period. Here, we formally report the genome of C. parasitica EP155 using a Sanger shotgun sequencing approach. After finishing and integration with simple-sequence repeat markers, the assembly was 43.8 Mb in 26 scaffolds (L50 = 5; N50 = 4.0Mb). Eight chromosomes are predicted: five scaffolds have two telomeres and six scaffolds have one telomere sequence. In total, 11,609 gene models were predicted, of which 85% show similarities to other proteins. This genome resource has already increased the utility of a fundamental plant pathogen experimental system through new understanding of the fungal vegetative incompatibility system, with significant implications for enhancing mycovirus-based biological control.

Published
2020
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7. Genome Sequence of the Chestnut Blight Fungus

Author

Jo Anne, Crouch, Angus, Dawe, Andrea, Aerts, Kerrie, Barry, Alice C L, Churchill, Jane, Grimwood, Bradley I, Hillman, Michael G, Milgroom, Jasmyn, Pangilinan, Myron, Smith, Asaf, Salamov, Jeremy, Schmutz, Jagjit S, Yadav, Igor V, Grigoriev, and Donald L, Nuss

Subjects
Ascomycota, North America, Fungal Viruses, Fagaceae, Plant Diseases
Published
2020

8. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.

Author

Stephen B Goodwin, Sarrah Ben M'barek, Braham Dhillon, Alexander H J Wittenberg, Charles F Crane, James K Hane, Andrew J Foster, Theo A J Van der Lee, Jane Grimwood, Andrea Aerts, John Antoniw, Andy Bailey, Burt Bluhm, Judith Bowler, Jim Bristow, Ate van der Burgt, Blondy Canto-Canché, Alice C L Churchill, Laura Conde-Ferràez, Hans J Cools, Pedro M Coutinho, Michael Csukai, Paramvir Dehal, Pierre De Wit, Bruno Donzelli, Henri C van de Geest, Roeland C H J van Ham, Kim E Hammond-Kosack, Bernard Henrissat, Andrzej Kilian, Adilson K Kobayashi, Edda Koopmann, Yiannis Kourmpetis, Arnold Kuzniar, Erika Lindquist, Vincent Lombard, Chris Maliepaard, Natalia Martins, Rahim Mehrabi, Jan P H Nap, Alisa Ponomarenko, Jason J Rudd, Asaf Salamov, Jeremy Schmutz, Henk J Schouten, Harris Shapiro, Ioannis Stergiopoulos, Stefano F F Torriani, Hank Tu, Ronald P de Vries, Cees Waalwijk, Sarah B Ware, Ad Wiebenga, Lute-Harm Zwiers, Richard P Oliver, Igor V Grigoriev, and Gert H J Kema

Subjects
Genetics, QH426-470
Abstract

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed "mesosynteny" is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors.

Published
2011
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9. Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

Author

Igor V. Grigoriev, Youzhi Miao, Alexey G. Kopchinskiy, Irina S. Druzhinina, Kurt LaButti, Shadi Pourmehdi, Asaf Salamov, Kamariah Abu Salim, Kerrie Barry, Jian Zhang, Lea Atanasova, Mohammad Javad Rahimi, Bernard Henrissat, Hope Hundley, Qirong Shen, Alan Kuo, Anna Lipzen, Komal Chenthamara, Feng Cai, Christian P. Kubicek, Marica Grujic, Andrea Aerts, Carina Pretzer, Dongqing Yang, Mei Wang, Research Area Biotechnology and Microbiology, Technical University of Vienna [Vienna] (TU WIEN)-Institute of Chemical Engineering, Technische Universität Wien (TU Wien), Laboratoire de Linguistique Formelle (LLF UMR7110), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Nanjing Agricultural University, Fac Sci, Environm & Life Sci, University of Brunei Darussalam (Biology Department), Universiti Brunei Darussalam, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), US Department of Energy Joint Genome Institute, U.S Department of Energy, U.S. Department of Energy (DOE)-U.S. Department of Energy (DOE), Dept Energy Great Lakes Bioenergy Res Ctr, Joint Genome institute, United States Department of Energy, Joint Genome Institute, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), ANR-17-CE34-0002,EMBRASE,Environnement MicroBiologique et Risque Allergique, Suivi des Enfants à 5 ans(2017), Vienna University of Technology (TU Wien)-Institute of Chemical Engineering, Vienna University of Technology (TU Wien), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Nanjing Agricultural University (NAU), U.S. Department of Energy [Washington] (DOE)-U.S. Department of Energy [Washington] (DOE), Austrian Science Fund (FWF) [P 25613 B20], Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231], National Natural Science Foundation of China [31330069], Chinese Ministry of Science and Technology (973 Program) [2015CB150500], IDEX Aix-Marseille (Grant Microbio-E), Kuala Belalong Field Studies Centre [WWTF-LS13-048], Martin, Francis, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Druzhinina, Irina S., and Shen, Qirong

Subjects
0301 basic medicine, Cancer Research, Gene Transfer, genome sequence, phylogenetic analysis, transplant recipient, multiple alignments, dna polymorphism, pythium-ultimum, life-style, web server, evolution, reesei, Fungal genetics, Cell Wall, Scanning, Fungal genomics, Genetics (clinical), Phylogeny, Data Management, 2. Zero hunger, Trichoderma, Fungal protein, Microscopy, Phylogenetic analysis, biology, Ascomycota, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Eukaryota, food and beverages, Basidiomycota, Genomics, Plants, Phylogenetics, Parasite evolution, Host-Pathogen Interactions, Hypocreales, Biotechnology, Research Article, Computer and Information Sciences, Hypha, lcsh:QH426-470, Gene Transfer, Horizontal, Glycoside Hydrolases, Hyphae, Fungus, Mycology, Electron, complex mixtures, Horizontal, Fungal Proteins, 03 medical and health sciences, Botany, Genetics, Evolutionary Systematics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Taxonomy, Evolutionary Biology, fungi, Organisms, technology, industry, and agriculture, Fungi, Biology and Life Sciences, 15. Life on land, biology.organism_classification, Ascomycetes, lcsh:Genetics, 030104 developmental biology, Microscopy, Electron, Scanning, Parasitology, Fungal evolution, Developmental Biology
Abstract

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass., Author summary Individual fungi rely on particular host organisms or substrates for their nutrition. Therefore, the genomes of fungi feeding on plant biomass necessarily contain genes encoding plant cell wall-degrading enzymes, while animal parasites may depend on proteolytic activity. Molds in the genus Trichoderma (Ascomycota) display a unique nutritional versatility. They can feed on other fungi, attack animals, and degrade plant debris. The later property is so efficient that one species (T. reesei) is commercially used for the production of cellulolytic enzymes required for making biofuels and other industry. In this work, we have investigated the evolution of proteins required for plant cell wall degradation in nine Trichoderma genomes and found an unprecedented number of lateral gene transfer (LGT) events for genes encoding these enzymes. Interestingly, the transfers specifically occurred from Ascomycota molds that feed on plants. We detected no cases of LGT from other fungi (e.g., mushrooms or wood-rotting fungi from Basidiomycota) that are frequent hosts of Trichoderma. Therefore, we propose that LGT may be linked to the ability of Trichoderma to parasitize on related organisms. This is a characteristic ecological trait that distinguishes Trichoderma from other mycoparasitic fungi. In this report, we demonstrate that the lateral transfer of genes may result in a profound nutritional expansion and contribute to the emergence of a generalist capable of feeding on organic matter of any origin.

Published
2018
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10. The fungus that came in from the cold:dry rot's pre-adapted ability to invade buildings

Author

Kurt LaButti, Daniel C. Eastwood, Nils Högberg, Igor V. Grigoriev, Lynne Boddy, Andrea Aerts, Cinzia Progida, S. C. Moody, Håvard Kauserud, Inger Skrede, Sudhagar V. Balasundaram, Mikael Brandström Durling, Kerrie Barry, Jaqueline Hess, and Lisbeth Thorbek

Subjects
0301 basic medicine, Hyphal growth, Technology, 030106 microbiology, Adaptation, Biological, Fungus, Microbiology, complex mixtures, Article, 03 medical and health sciences, Botany, Temperate climate, Humans, Adaptation, Ecosystem, Ecology, Evolution, Behavior and Systematics, Ecological niche, Water transport, biology, Construction Materials, Basidiomycota, fungi, technology, industry, and agriculture, Genetic Variation, DNA, Sequence Analysis, DNA, Biological Sciences, Biological, biology.organism_classification, Wood, 030104 developmental biology, Habitat, Dry rot, Sequence Analysis, Environmental Sciences, Serpula lacrymans
Abstract

Many organisms benefit from being pre-adapted to niches shaped by human activity, and have successfully invaded man-made habitats. One such species is the dry rot fungus Serpula lacrymans, which has a wide distribution in buildings in temperate and boreal regions, where it decomposes coniferous construction wood. Comparative genomic analyses and growth experiments using this species and its wild relatives revealed that S. lacrymans evolved a very effective brown rot decay compared to its wild relatives, enabling an extremely rapid decay in buildings under suitable conditions. Adaptations in intracellular transport machineries promoting hyphal growth, and nutrient and water transport may explain why it is has become a successful invader of timber in houses. Further, we demonstrate that S. lacrymans has poor combative ability in our experimental setup, compared to other brown rot fungi. In sheltered indoor conditions, the dry rot fungus may have limited encounters with other wood decay fungi compared to its wild relatives. Overall, our analyses indicate that the dry rot fungus is an ecological specialist with poor combative ability against other fungi.

Published
2018
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11. Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

Author

Erika Lindquist, Richard C. Hamelin, Nicolas Feau, Jasmyn Pangilinan, Bernard Henrissat, Andrea Aerts, Braham Dhillon, Navdeep Gill, Padmini Herath, Ronald P. de Vries, Philippe Tanguay, Eline Majoor, Monique L. Sakalidis, John N. Saddler, Igor V. Grigoriev, Adam Foster, Kurt LaButti, Robin A. Ohm, Amadeus Pribowo, Anthony Levasseur, Stéphanie Beauseigle, Stephen B. Goodwin, Alex Copeland, Louis Bernier, Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Sub Molecular Plant Physiology, Sub Molecular Microbiology, and Molecular Plant Physiology

Subjects
Time Factors, Colony Count, Gene Transfer, Septoria canker, Colony Count, Microbial, Gene Dosage, Indole Alkaloids, Trees, Microbial, Gene Expression Regulation, Fungal, Gene cluster, Fungal genomics, ComputingMilieux_MISCELLANEOUS, Phylogeny, Genome, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Ascomycota, biology, food and beverages, Poplar pathogen, Biological Sciences, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Adaptation, Physiological, Wood, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Fungal, Populus, Host-Pathogen Interactions, Horizontal gene transfer, Mycosphaerella, Genome, Fungal, Woody plant, Gene Transfer, Horizontal, Genetic Speciation, Nitrogen, Physiological, Molecular Sequence Data, Synteny, Gene dosage, Horizontal, Tree disease, Botany, medicine, Adaptation, General, Gene, Canker, Base Sequence, fungi, biology.organism_classification, medicine.disease, Gene Expression Regulation, Proteolysis
Abstract

Some of the most damaging tree pathogens can attack woody stems, causing lesions (cankers) that may be lethal. To identify the genomic determinants of wood colonization leading to canker formation, we sequenced the genomes of the poplar canker pathogen, Mycosphaerella populorum, and the closely related poplar leaf pathogen, M. populicola. A secondary metabolite cluster unique to M. populorum is fully activated following induction by poplar wood and leaves. In addition, genes encoding hemicellulose-degrading enzymes, peptidases, and metabolite transporters were more abundant and were up-regulated in M. populorum growing on poplar wood-chip medium compared with M. populicola. The secondary gene cluster and several of the carbohydrate degradation genes have the signature of horizontal transfer from ascomycete fungi associated with wood decay and from prokaryotes. Acquisition and maintenance of the gene battery necessary for growth in woody tissues and gene dosage resulting in gene expression reconfiguration appear to be responsible for the adaptation of M. populorum to infect, colonize, and cause mortality on poplar woody stems.

Published
2015
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12. Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships

Author

Sayaji T. Mehetre, Irina S. Druzhinina, Igor V. Grigoriev, Ravindra Bansal, Andrea Aerts, Prasun K. Mukherjee, Sonia Chadha, and Alan Kuo

Subjects
0106 biological sciences, 0301 basic medicine, Cytochrome, lcsh:Biotechnology, Computational biology, 01 natural sciences, Applied Microbiology and Biotechnology, Genome, 03 medical and health sciences, chemistry.chemical_compound, Mycology, lcsh:TP248.13-248.65, Genetics, Secondary metabolism, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Organism, chemistry.chemical_classification, biology, Research, Human Genome, Cell Biology, 030104 developmental biology, Enzyme, chemistry, biology.protein, Xenobiotic, Function (biology), 010606 plant biology & botany, Biotechnology
Abstract

Background Cytochrome P450s form an important group of enzymes involved in xenobiotics degradation and metabolism, both primary and secondary. These enzymes are also useful in industry as biotechnological tools for bioconversion and a few are reported to be involved in pathogenicity. Trichoderma spp. are widely used in industry and agriculture and are known for their biosynthetic potential of a large number of secondary metabolites. For realising the full biosynthetic potential of an organism, it is important to do a genome-wide annotation and cataloguing of these enzymes. Results Here, we have studied the genomes of seven species (T. asperellum, T. atroviride, T. citrinoviride, T. longibrachiatum, T. reesei , T. harzianum and T. virens) and identified a total of 477 cytochrome P450s. We present here the classification, evolution and structure as well as predicted function of these proteins. This study would pave the way for functional characterization of these groups of enzymes and will also help in realization of their full economic potential. Conclusion Our CYPome annotation and evolutionary studies of the seven Trichoderma species now provides opportunities for exploration of research-driven strategies to select Trichoderma species for various applications especially in relation to secondary metabolism and degradation of environmental pollutants. Electronic supplementary material The online version of this article (10.1186/s40694-018-0056-3) contains supplementary material, which is available to authorized users.

Published
2018
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13. Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12

Author

Kurt LaButti, David S. Hibbett, Igor V. Grigoriev, Matt Nolan, Debbie Yaver, Kerrie Barry, Dan Cullen, Jagjit S. Yadav, Emma R. Master, Anna Lipzen, Cindy Chen, Kathleen Lail, Randy M. Berka, Robert A. Blanchette, Ángel T. Martínez, Paulo Canessa, Diego Martinez, Phil Kersten, Bernard Henrissat, Jon K. Magnuson, Robert Riley, Christian P. Kubicek, Luis F. Larrondo, Jill Gaskell, Andrea Aerts, Monika Schmoll, Pontificia Universidad Católica de Chile (UC), Universidad de Castilla-La Mancha = University of Castilla-La Mancha (UCLM), Clark University, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231], AMIDEX foundation (MicrobioE project) [ANR-11-IDEX-0001-02], Cullen, Dan, Department of Energy (US), Universidad de Castilla-La Mancha (UCLM), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)

Subjects
0301 basic medicine, lcsh:QH426-470, 030106 microbiology, Rhodonia placenta, macromolecular substances, Biochemistry, complex mixtures, Postia placenta, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Data in Brief, Genetics, Theology, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, biology, technology, industry, and agriculture, Monokaryon, food and beverages, biology.organism_classification, 3. Good health, lcsh:Genetics, 030104 developmental biology, Molecular Medicine, Postia, Biotechnology
Abstract

3 p.-2 tab. Gaskell, Jill et al., We report the genome of Postia (Rhodonia) placenta MAD-SB12, a homokaryotic wood decay fungus (Basidiomycota, Polyporales). Intensively studied as a representative brown rot decayer, the gene complement is consistent with the rapid depolymerization of cellulose but not lignin., The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. BH was funded by the AMIDEX foundation (MicrobioE project, grant number ANR-11-IDEX-0001-02).

Published
2017
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14. Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control

Author

Claudia Fortes Fereira, Jeremy Schmutz, Richard C. Hamelin, Andrew Farmer, Theo van der Lee, Charles F. Crane, Robert A. Dietrich, Olman Quiros, Ineke de Vries, Rahim Mehrabi, Lute Harm Zwiers, Gabriel Scalliet, Andrea Aerts, Manoel Souza, Harris Shapiro, Braham Dhillon, Caucasella Diaz-Trujillo, Rafael Arango Isaza, Erika Lindquist, Gert H. J. Kema, Elizabeth Reynolds, Tristan V. de Jong, Mauricio Guzman, Suzana Garcia, Pierre J. G. M. de Wit, M.F. Zapater, Ioannis Stergiopoulos, Stephen B. Goodwin, Igor V. Grigoriev, Jean Carlier, and McDowell, John M

Subjects
Résistance génétique, Musa (bananes), Breeding, Pathology and Laboratory Medicine, Musa acuminata, Mobile Genetic Elements, 2.2 Factors relating to the physical environment, Aetiology, Disease Resistance, Fungal Pathogens, Contrôle de maladies, food and beverages, Genomics, Plants, Fungal, Medical Microbiology, Chromosomes, Fungal, Genome, Fungal, Maladie des raies noires, Infection, ELECTROPHORETIC KARYOTYPE, LEAF STREAK DISEASE, Genotype, GENETIC-STRUCTURE, Microbiology, 03 medical and health sciences, Ascomycota, Botany, Genetics, Mycosphaerella fijiensis, Caryotype, Fungal Genetics, Variété, Bioint Diagnostics, Food Safety & Phyt. Research, Molecular Biology, Microbial Pathogens, Ecology, Evolution, Behavior and Systematics, Fungal Genomics, H20 - Maladies des plantes, Plant Diseases, LTR RETROTRANSPOSONS, Organisms, Biology and Life Sciences, Computational Biology, Correction, Genetic Variation, LEPTOSPHAERIA-MACULANS, Plant Pathology, Amélioration des plantes, Laboratorium voor Phytopathologie, 030104 developmental biology, Laboratory of Phytopathology, TRANSPOSABLE ELEMENTS, EPS, CAUSAL AGENT, Developmental Biology, 0301 basic medicine, Phylogénie, Cancer Research, Black sigatoka, INDUCED POINT MUTATIONS, Bananas, Genome, F30 - Génétique et amélioration des plantes, Pseudocercospora, Leptosphaeria maculans, Bioint Diagnostics, Medicine and Health Sciences, Genetics (clinical), biology, Chromosome Biology, Entomology & Disease Management, Fungal genetics, Agriculture, DE-NOVO IDENTIFICATION, Fungicide, Food Safety & Phyt. Research, Mycosphaerella, Pathogens, Research Article, Retroelements, lcsh:QH426-470, Crops, Mycology, Chromosomes, Fruits, Biointeractions and Plant Health, Genetic Elements, EUKARYOTIC GENOMES, Life Science, Génie génétique, Genetic diversity, Génome, Human Genome, Fungi, Musa, Cell Biology, Comparative Genomics, Résistance aux maladies, biology.organism_classification, Plant Leaves, lcsh:Genetics, Gène, Crop Science
Abstract

Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus Pseudocercospora fijiensis (previously: Mycosphaerella fijiensis), is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase the economic and environmental costs to produce banana. Weekly applications in most banana plantations lead to rapid evolution of fungicide-resistant strains within populations causing disease-control failures throughout the world. Given its extremely high economic importance, two strains of P. fijiensis were sequenced and assembled with the aid of a new genetic linkage map. The 74-Mb genome of P. fijiensis is massively expanded by LTR retrotransposons, making it the largest genome within the Dothideomycetes. Melting-curve assays suggest that the genomes of two closely related members of the Sigatoka disease complex, P. eumusae and P. musae, also are expanded. Electrophoretic karyotyping and analyses of molecular markers in P. fijiensis field populations showed chromosome-length polymorphisms and high genetic diversity. Genetic differentiation was also detected using neutral markers, suggesting strong selection with limited gene flow at the studied geographic scale. Frequencies of fungicide resistance in fungicide-treated plantations were much higher than those in untreated wild-type P. fijiensis populations. A homologue of the Cladosporium fulvum Avr4 effector, PfAvr4, was identified in the P. fijiensis genome. Infiltration of the purified PfAVR4 protein into leaves of the resistant banana variety Calcutta 4 resulted in a hypersensitive-like response. This result suggests that Calcutta 4 could carry an unknown resistance gene recognizing PfAVR4. Besides adding to our understanding of the overall Dothideomycete genome structures, the P. fijiensis genome will aid in developing fungicide treatment schedules to combat this pathogen and in improving the efficiency of banana breeding programs., Author Summary Black Sigatoka or black leaf streak disease, caused by the ascomycete fungus Pseudocercospora fijiensis, inflicts huge costs on banana producers, due to crop losses and expenses for disease control. The global banana export trade relies on Cavendish clones that are highly susceptible to P. fijiensis. Sustainable production of the world’s number one fruit requires a better understanding of host resistance and sophisticated management of fungicide resistance in the pathogen. In the P. fijiensis genome sequence we identified an effector that induced an HR-like necrosis on a resistant banana accession but not on a susceptible cultivar. If validated, this assay may be useful for identifying resistance in banana breeding programs. We also used the genomic sequence to develop highly polymorphic molecular markers for analyzing P. fijiensis field populations and identified a strong enrichment (nearly 100%) for fungicide resistance markers in fungicide-treated banana plantations compared to untreated wild-type populations. This rapid evolution of fungicide resistance poses an immediate threat to sustainable banana production.

Published
2016
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15. The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties

Author

Jure Piškur, Marina Marcet-Houben, Trevor G. Phister, Concetta Compagno, Olena P. Ishchuk, Kurt LaButti, Zhihao Ling, Toni Gabaldón, Kerrie Barry, Igor V. Grigoriev, Alex Copeland, Linda F. Bisson, Andrea Aerts, and Erika Lindquist

Subjects
Saccharomyces cerevisiae, Brettanomyces, Brettanomyces bruxellensis, Wine, Microbiology, Genome, Pichia, Phenols, Yeasts, Botany, Gene, Phylogeny, Comparative genomics, Genetics, Dekkera, Ethanol, biology, Alcohol Dehydrogenase, food and beverages, General Medicine, biology.organism_classification, Biological Evolution, Yeast, Yeast in winemaking, Saccharomycetales, Food Science
Abstract

The yeast Dekkera/Brettanomyces bruxellensis can cause enormous economic losses in wine industry due to production of phenolic off-flavor compounds. D. bruxellensis is a distant relative of baker's yeast Saccharomyces cerevisiae. Nevertheless, these two yeasts are often found in the same habitats and share several food-related traits, such as production of high ethanol levels and ability to grow without oxygen. In some food products, like lambic beer, D. bruxellensis can importantly contribute to flavor development. We determined the 13.4 Mb genome sequence of the D. bruxellensis strain Y879 (CBS2499) and deduced the genetic background of several "food-relevant" properties and evolutionary history of this yeast. Surprisingly, we find that this yeast is phylogenetically distant to other food-related yeasts and most related to Pichia (Komagataella) pastoris, which is an aerobic poor ethanol producer. We further show that the D. bruxellensis genome does not contain an excess of lineage specific duplicated genes nor a horizontally transferred URA1 gene, two crucial events that promoted the evolution of the food relevant traits in the S. cerevisiae lineage. However, D. bruxellensis has several independently duplicated ADH and ADH-like genes, which are likely responsible for metabolism of alcohols, including ethanol, and also a range of aromatic compounds.

Published
2012
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16. Massive Changes in Genome Architecture Accompany the Transition to Self-Fertility in the Filamentous Fungus Neurospora tetrasperma

Author

Donald O. Natvig, Igor V. Grigoriev, Brian Foster, Erika Lindquist, John W. Taylor, Christopher E. Ellison, Alla Lapidus, Andrea Aerts, David J. Jacobson, Jason E. Stajich, and Robert Riley

Subjects
0106 biological sciences, Transposable element, Mating type, Locus (genetics), Investigations, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Genome Integrity and Transmission, 03 medical and health sciences, Genetics, Ectopic recombination, Codon, Gene, 030304 developmental biology, Gene Rearrangement, Recombination, Genetic, 0303 health sciences, Gene rearrangement, Genes, Mating Type, Fungal, Neurospora, Fertility, Chromosomes, Fungal, Genome, Fungal, Recombination
Abstract

A large region of suppressed recombination surrounds the sex-determining locus of the self-fertile fungus Neurospora tetrasperma. This region encompasses nearly one-fifth of the N. tetrasperma genome and suppression of recombination is necessary for self-fertility. The similarity of the N. tetrasperma mating chromosome to plant and animal sex chromosomes and its recent origin (

Published
2011
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17. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

Author

M. Meijer, Herman Jan Pel, Jasmyn Pangilinan, Jette Thykaer, Gerhard H. Braus, Scott E. Baker, Rob Samson, Jens Christian Frisvad, Kristian Fog Nielsen, Erika Lindquist, Susanna A. Braus-Stromeyer, Margarita Salazar, Peter J. I. van de Vondervoort, Peter J. Schaap, Michael Lynge Nielsen, Diego Martinez, Susan Lisette Meijer, Johannes Maarten Van Den Brink, Jakob Blæsbjerg Nielsen, Johannes Andries Roubos, Hein Stam, Jon K. Magnuson, Noël Nicolaas Maria Elisabeth Van Peij, Lars Kongsbak Poulsen, Adrian Tsang, Alex Atkins, Asaf Salamov, Ziyu Dai, Jane Grimwood, Harris Shapiro, Igor V. Grigoriev, Piet W.M. van Dijck, Susan Lucas, Andrea Aerts, Luis M. Corrochano, Hildegard Henna Menke, Albert J. J. van Ooyen, David E. Culley, Gerald Hofmann, Mikael Rørdam Andersen, Randy M. Berka, Jens Nielsen, Linda L. Lasure, Yigong Lou, Kaj Albermann, Christian P. Kubicek, Richard Albang, and Universidad de Sevilla. Departamento de Genética

Subjects
Genome, Citric acid, Glucan 1, liquid-chromatography, Systems and Synthetic Biology, Phylogeny, Genetics (clinical), Gene Rearrangement, 2. Zero hunger, Genetics, Systeem en Synthetische Biologie, 0303 health sciences, biology, Fungal genetics, Genomics, saccharomyces-cerevisiae, Aspergillus niger, Genome, Fungal, Transfer RNA, recognition, Gene Transfer, Horizontal, Sequence analysis, Molecular Sequence Data, linkage group, Polymorphism, Single Nucleotide, Synteny, Evolution, Molecular, 03 medical and health sciences, Species Specificity, mycotoxins, expression, 4 alpha glucosidase, Gene, VLAG, 030304 developmental biology, Whole genome sequencing, Comparative genomics, Base Sequence, 030306 microbiology, Research, Gene Expression Profiling, Computational Biology, Genetic Variation, fungal metabolite, Sequence Analysis, DNA, biology.organism_classification, karyotype, gene ontology, identification
Abstract

The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.

Published
2011
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18. Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

Author

Robert Otillar, Olivier Panaud, Aaron Poliakov, Ian T. Paulsen, Eve Toulza, Steven Robbens, Heidrun Gundlach, Pedro M. Coutinho, E. Virginia Armbrust, Jill E. Gready, Klaus F. X. Mayer, Jasmyn Pangilinan, Kemin Zhou, Igor V. Grigoriev, Wenche Eikrem, Marie L. Cuvelier, Elif Demir, Ursula Goodenough, Jonathan H. Badger, Hervé Moreau, Susan Lucas, Peter von Dassow, Yves Van de Peer, Evelyne Derelle, Pierre Rouzé, Andrew E. Allen, Erika Lindquist, Uwe John, Elodie Foulon, Jeremy Schmutz, Fabrice Not, William Lanier, Meredith V. Everett, Alex N. Zelensky, Sarah M. McDonald, Benoît Piégu, Jane Grimwood, Tania Wyss, Chelle L. Gentemann, Aasf Salamov, Micaela S. Parker, Stephane Rombauts, Alexandra Z. Worden, Carolyn A. Napoli, Thomas Mock, Bernard Henrissat, Jae-Hyeok Lee, Inna Dubchak, Melinda P. Simmons, Andrea Aerts, Debashish Bhattacharya, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, School of Oceanography [Seattle], University of Washington [Seattle], Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Biology Institute, University of Arizona, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, Stanford University School of Medicine [Stanford], Stanford University [Stanford], and Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, MESH: Sequence Analysis, DNA, RNA, Untranslated, MESH: Oceans and Seas, MESH: Introns, MESH: Plants, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Genome, 18S ribosomal RNA, Bathycoccus, MESH: Chlorophyta, MESH: RNA, Untranslated, Chlorophyta, MESH: Ecosystem, MESH: Genetic Variation, Photosynthesis, MESH: Phylogeny, Clade, Phylogeny, MESH: Photosynthesis, Plant evolution, 0303 health sciences, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], MESH: Transcription Factors, Plants, Adaptation, Physiological, Biological Evolution, MESH: Gene Expression Regulation, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Genes, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Meiosis, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], MESH: DNA Transposable Elements, Oceans and Seas, Molecular Sequence Data, MESH: Biological Evolution, Genomics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Ecosystem, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, Micromonas, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Repetitive Sequences, Nucleic Acid, MESH: Molecular Sequence Data, Genetic Variation, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Sequence Analysis, DNA, biology.organism_classification, MESH: Adaptation, Physiological, Introns, MESH: Meiosis, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Gene Expression Regulation, Genes, Phytoplankton, DNA Transposable Elements, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Transcription Factors, MESH: Phytoplankton, 010606 plant biology & botany
Abstract

Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18 S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.

Published
2009
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19. The DNA sequence and comparative analysis of human chromosome 5

Author

Nancy Hammon, Arthur Kobayashi, Stacey Black, Uffe Hellsten, Daniel S. Rokhsar, Lauren Haydu, Frederick Lopez, Nina Thayer, Diego Martinez, Mirian Denys, Paul Predki, Laurie Gordon, Eva Bajorek, Eidelyn Gonzales, Catherine Medina, Richard D. Nandkeshwar, Sanjay Israni, Richard M. Myers, Hope Tice, Jean F. Challacombe, Anne O. Olsen, Chenier Caoile, State Lowry, Alex Rodriguez, Paul G. Richardson, Kevin Wu, D. Scott, Xinwei She, Matthew Groza, James P. Noonan, Anna Ustaszewska, María Laura Ríos Gómez, Jane Grimwood, Jeremy Wheeler, Len A. Pennacchio, Martin O. Pollard, Tijana Glavina, Dea Fotopulos, Joel Martin, Heather Kimbal, Kristen Kadner, Dave Flowers, Joan Yang, Astrid Terry, Lucía Ramírez, Ming Tsai, Yee Man Chan, Michael R. Altherr, Susan Lucas, Jan Fang Cheng, Sam Pitluck, Sam Rash, Igor V. Grigoriev, Wayne Huang, Yunian Lou, Chris Detter, Shyam Prabhakar, James Priest, Angelica Salazar, Gary Xie, Nu Vo, Elbert Branscomb, Jamie Jett, Stephanie Rogers, David Goodstenin, Olivier Couronne, Julio Escobar, James Retterer, Mary Bao Tran-Gyamfi, Trevor Hawkins, Jeremy Schmutz, Evan E. Eichler, Andrea Aerts, Mark Dickson, Jenna Morgan, Edward M. Rubin, and Asaf Salamov

Subjects
Pan troglodytes, Molecular Sequence Data, Biology, Synteny, Muscular Atrophy, Spinal, Complete sequence, Chromosome 15, Gene Duplication, Chromosome 19, Animals, Humans, Conserved Sequence, Chromosome 12, Genetics, Chromosome 7 (human), Base Composition, Multidisciplinary, Interleukins, Genetic Diseases, Inborn, Genomics, Sequence Analysis, DNA, Cadherins, Physical Chromosome Mapping, Chromosome 17 (human), Genes, Vertebrates, Chromosomes, Human, Pair 5, Chromosome 21, Pseudogenes
Abstract

Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding conservation with non-mammalian vertebrates, suggesting that they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. We also completely sequenced versions of the large chromosome-5-specific internal duplications. These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy.

Published
2004
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20. Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii

Author

Neil F. W. Saunders, John S. Mattick, Kevin R. Sowers, Robert A. Feldman, Miriam Land, Paul G. Richardson, Shellie R. Bench, Karl Rusterholtz, Frank W. Larimer, Peter D. Franzmann, Andrea Aerts, Ricardo Cavicchioli, David Boone, Chris Gates, Torsten Thomas, Paul M. G. Curmi, Susan Lucas, Kristen Kadner, Tijana Glavina, Elizabeth Kuczek, Loren Hauser, Chris Detter, Paramvir S. Dehal, John Davis, and Rob Slade

Subjects
Models, Molecular, Archaeal Proteins, Molecular Sequence Data, Protein domain, Biology, Methanogenium frigidum, Genes, Archaeal, Protein structure, Bacterial Proteins, RNA, Transfer, Genome, Archaeal, Methanococcoides burtonii, Genetics, Amino Acid Sequence, Psychrophile, Genetics (clinical), Base Composition, Sequence Homology, Amino Acid, Thermophile, RNA-Binding Proteins, Methanosarcinaceae, Articles, biology.organism_classification, Adaptation, Physiological, Hyperthermophile, Cold Temperature, DNA-Binding Proteins, Biochemistry, Nucleic Acid Conformation, Methanomicrobiaceae, Archaea
Abstract

We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of noncharged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15°–98°C) were used to generate 1111 modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gln, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60°C, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles.

Published
2003
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21. Genome Sequences of Industrially Relevant Saccharomyces cerevisiae Strain M3707, Isolated from a Sample of Distillers Yeast and Four Haploid Derivatives

Author

Courtney M Johnson, Alicia Clum, Allan C. Froehlich, Igor V. Grigoriev, Kerrie Barry, Matthew Zane, Heidi Hau, Aditi Sharma, David A. Hogsett, Lee R. Lynd, Asaf Salamov, Andrea Aerts, Steven D. Brown, Paul Gilna, Brian H. Davison, and Dawn M. Klingeman

Subjects
Genetics, Whole genome sequencing, Eukaryotes, Strain (biology), Saccharomyces cerevisiae, Biology, biology.organism_classification, Genome, Yeast, Microbiology, Biomass fuels, Ploidy, Bioprocess, Molecular Biology
Abstract

Saccharomyces cerevisiae strain M3707 was isolated from a sample of commercial distillers yeast, and its genome sequence together with the genome sequences for the four derived haploid strains M3836, M3837, M3838, and M3839 has been determined. Yeasts have potential for consolidated bioprocessing (CBP) for biofuel production, and access to these genome sequences will facilitate their development.

Published
2013

22. The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

Author

Rahim Mehrabi, Ronald P. de Vries, Andrea Aerts, Hui Sun, Pierre J. G. M. de Wit, Erwin Datema, M. Shahjahan Kabir, Richard C. Hamelin, Anthony Levasseur, Kamel A. Abd-Elsalam, Erika Lindquist, Ali H. Bahkali, Igor V. Grigoriev, Henriek G. Beenen, Murray P. Cox, Rosie E. Bradshaw, Alla Lapidus, Scott A. Griffiths, Ioannis Stergiopoulos, Pranav Chettri, Bernard Henrissat, Elio Schijlen, Robin A. Ohm, Yanan Guo, Sylvia Klaubauf, Roeland C. H. J. van Ham, Austen R. D. Ganley, Jérôme Collemare, Shuguang Zhang, Braham Dhillon, Bilal Ökmen, Gert H. J. Kema, Ate van der Burgt, Arne Schwelm, Timothy J. Owen, Harrold A. van den Burg, Asaf Salamov, Mansoor Karimi Jashni, Stephen B. Goodwin, Green Life Sciences, Molecular Plant Pathology (SILS, FNWI), Phytopathol Lab, Wageningen University and Research [Wageningen] (WUR), Ctr BioSyst Genom, Lab Bioinformat, Dept Plant Pathol, University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Agr Res Ctr, Plant Pathology Research Institute, Joint Genome Inst, United States Department of Energy, King Saud University [Riyadh] (KSU), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Biodiversité et Biotechnologie Fongiques (BBF), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Wageningen University, Royal Netherlands Academy of Arts and Sciences, Centre for Biosystems Genomics, European Research Area-Plant Genomics, Willie Commelin Scholten Foundation, Graduate School of Experimental Plant Sciences, Massey University, New Zealand Bio-Protection Research Centre, Royal Society of New Zealand, Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231], European Project: 27649,ERA-PG, University of California-University of California, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Wageningen University and Research Centre [Wageningen] (WUR), and École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Cancer Research, FUSIFORM RUST DISEASE, [SDV]Life Sciences [q-bio], Plant Science, Gene prediction, Passalora fulva, 01 natural sciences, Genome, aspergillus-nidulans, mating-type genes, Solanum lycopersicum, Fungal genetics, Gene Expression Regulation, Fungal, CELL-WALL, Fungal genomics, leaf mold, Genetics (clinical), Phylogeny, MATING-TYPE GENES, Genetics, 0303 health sciences, biology, Effector, leptosphaeria-maculans, fusiform rust disease, INDUCED POINT MUTATION, Genomics, Adaptation, Physiological, Functional Genomics, cell-wall, Host-Pathogen Interactions, ASPERGILLUS-NIDULANS, Cladosporium, Research Article, Hypersensitive response, lcsh:QH426-470, Bioinformatics, forest pathogen, AVIRULENCE GENE AVR9, NEEDLE BLIGHT, LEPTOSPHAERIA-MACULANS, FOREST PATHOGEN, LEAF MOLD, Mycology, Microbiology, Molecular Genetics, Fungal Proteins, BIOS Applied Bioinformatics, 03 medical and health sciences, Tomatoes, Bioinformatica, needle blight, Biology, Molecular Biology, Gene, Plant fungal pathogens, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Plant Diseases, Base Sequence, Bioint Moleculair Phytopathology, Fungi, Computational Biology, Correction, Genome analysis, Comparative Genomics, Plant Pathology, induced point mutation, biology.organism_classification, Pinus, Laboratorium voor Phytopathologie, lcsh:Genetics, Laboratory of Phytopathology, Structural Genomics, Gene expression, avirulence gene avr9, 010606 plant biology & botany
Abstract

We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an α-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation., Author Summary We compared the genomes of two closely related pathogens with very different lifestyles and hosts: C. fulvum (Cfu), a biotroph of tomato, and D. septosporum (Dse), a hemibiotroph of pine. Some differences in gene content were identified that can be directly related to their different hosts, such as the presence of a gene involved in degradation of a tomato saponin only in Cfu. However, in general the two species share a surprisingly large proportion of genes. Dse has functional homologs of Cfu effector genes, while Cfu has genes for biosynthesis of dothistromin, a toxin probably associated with virulence in Dse. Cfu also has an unexpectedly large content of genes for biosynthesis of other secondary metabolites and degradation of plant cell walls compared to Dse, contrasting with its host preference and lifestyle. However, many of these genes were not expressed in planta or were pseudogenized. These results suggest that evolving species may retain genetic signatures of the host and lifestyle preferences of their ancestor and that evolution of new genes, gene regulation, and pseudogenization are important factors in adaptation.

Published
2012
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23. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

Author

László Nagy, Luis F. Larrondo, Daniel C. Eastwood, Ad Wiebenga, Ángel T. Martínez, Darcy Young, Isabelle Benoit, Chiaki Hori, Robert Riley, Erika Lindquist, Ronald P. de Vries, Grzegorz Sabat, Rachael Martin, Robin A. Ohm, Kurt LaButti, Dan Cullen, Pedro M. Coutinho, Susan Lucas, Alan Kuo, Vincent Lombard, Joel A. Jurgens, Jill Gaskell, Andrea Aerts, Jan Stenlid, Alexis Carlson, David S. Hibbett, Hui Sun, Brian Foster, Robert Otillar, Francisco J. Ruiz-Dueñas, Manfred Binder, Dylan Glotzer, Patricia Ferreira, Ingo Morgenstern, Francis Martin, Jason C. Slot, T. K. Arun Kumar, Matthew J Nolan, Taina Lundell, Phil Kersten, Aleksandrina Patyshakuliyeva, Khajamohiddin Syed, Antonis Rokas, Jagjit S. Yadav, Robert A. Blanchette, Franz J. St John, Jeremy Schmutz, Joseph W. Spatafora, Igor V. Grigoriev, Antonio G. Pisabarro, Emanuelle Morin, Sheng Sun, Albee Y. Ling, Bernard Henrissat, Adrian Tsang, Annegret Kohler, Dimitrios Floudas, Masahiro Samejima, Cedar N. Hesse, Alexander Boyd, Keisha Findley, Nathan M Kallen, Kerrie Barry, Kiyohiko Igarashi, Paweł Górecki, Claude Murat, Ursula Kües, Joseph Heitman, Asaf Salamov, Alex Copeland, David J. McLaughlin, Biology Department, Clark University, Joint Genome Institute, United States Department of Energy, Department of Plant Pathology, University of Minnesota [Twin Cities], University of Minnesota System-University of Minnesota System, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centro de investigaciones biológicas, Spanish National Research Council (CSIC), Department of Botany and Plant Pathology, Oregon State University (OSU), College of Medicine, Department of Environmental Health, Environmental Genetics and Molecular Toxicology Division, University of Cincinnati (UC), Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University [Utrecht], CBS-KNAW Fungal Biodiversity Centre, Department of Biochemistry and Molecular and Cellular Biology and Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Medical Center, Department of Molecular Genetics and Microbiology, Duke University [Durham], Forest Products Laboratory, United States Department of Agriculture, Institute of Informatics, University of Warsaw (UW), Graduate School of Agricultural and Life Sciences, Department of Biomaterial Sciences, The University of Tokyo, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Université Henri Poincaré - Nancy 1 (UHP), Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August-University [Göttingen], Department of Plant Biology, Facultad de Ciencias Biológicas, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile (UC), Viikki Plant Science Centre (ViPS), Faculty of Biological and Environmental Sciences [Helsinki], University of Helsinki-University of Helsinki, Centre for Structural and Functional Genomics, Concordia University [Montreal], Department of Biological Sciences, Vanderbilt University [Nashville], Biotechnology Center, University of Wisconsin, Hudson Alpha Institute for Biotechnology, Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences (SLU), Genetics and Microbiology Research Group, Public University of Navarre, College of Science, Swansea University, Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231], Assembling the Fungal Tree of Life (AFTOL) project under NSF [DEB-0732968, DEB-0732993, DEB-0732550], University of Minnesota [Twin Cities] (UMN), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institute of Informatics [Warsaw], Faculty of Mathematics, Informatics, and Mechanics [Warsaw] (MIMUW), University of Warsaw (UW)-University of Warsaw (UW), Graduate School of Agricultural and Life Sciences [UTokyo] (GSALS), The University of Tokyo (UTokyo), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), University of Wisconsin-Madison, Department of Forest Mycology and Plant Pathology, College of Science [Swansea], Georg-August-University = Georg-August-Universität Göttingen, Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA)

Subjects
Indoles, [SDV]Life Sciences [q-bio], Lineage (evolution), macromolecular substances, Fungus, Lignin, complex mixtures, Agaricomycetes, Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, Mycology, Agaricomycotina, Botany, Polyporales, 030304 developmental biology, 0303 health sciences, Multidisciplinary, biology, 030306 microbiology, Basidiomycota, fungi, technology, industry, and agriculture, food and beverages, Bayes Theorem, biology.organism_classification, Wood, Peroxidases, chemistry, Genome, Fungal
Abstract

5 páginas, 1 figura, 1 tabla, 22 figuras suplementarias, 16 tablas suplementarias -- PAGS nros. 1715-1719 et al., 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, The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-05CH11231. Also supported by the Assembling the Fungal Tree of Life (AFTOL) project under NSF awards DEB-0732968 (D.S.H.), DEB-0732993 (J.W.S.), and DEB-0732550 (D.J.M.).

Published
2012
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24. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

Author

Ari M. Hietala, Jeremy Schmutz, Yao-Cheng Lin, Pedro M. Coutinho, Vincent Lombard, Magnus Karlsson, Jane Grimwood, Linda T. A. van Diepen, Heriberto Vélëz, Ad Wiebenga, Timothy Y. James, Kerstin Dalman, Pierre Rouzé, Ourdia Bouzid, Tommaso Raffaello, Mikael Brandström Durling, Sébastien Duplessis, Karl Lundén, Susan Lucas, David Hansson, Carl Gunnar Fossdal, Andrea Aerts, Ursula Kües, Jerry Ståhlberg, Igor A. Yakovlev, Ronald P. de Vries, Erika Lindquist, Igor V. Grigoriev, Dirk Hoffmeister, Kajsa Himmelstrand, Yong-Hwan Lee, Matteo Garbelotto, Asaf Salamov, Dan Cullen, Mårten Lind, Björn Canbäck, Halvor Solheim, Nils Högberg, Paolo Gonthier, Francis Martin, Giuliana Deflorio, Emmanuelle Morin, Bernard Henrissat, Lassaad Belbahri, Christophe Dunand, Åke Olson, Jan Stenlid, Claude Murat, Steve Woodward, Annegret Kohler, Anders Broberg, Jongsun Park, Fred O. Asiegbu, Swedish University of Agricultural Sciences (SLU), Joint Genome Institute (JGI), University of Helsinki, Laboratory of Soil Biology, Université de Neuchâtel (UNINE), Utrecht University [Utrecht], Department of Chemistry, Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Forest Products Laboratory, University of Aberdeen, University of Michigan [Ann Arbor], University of Michigan System, Dynamique et Evolution des Parois cellulaires végétales, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Universita di Torino, Hudson Alpha Institute for Biotechnology, Norwegian Forest and Landscape Institute, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Georg-August-University [Göttingen], Seoul National University [Seoul] (SNU), Universiteit Gent = Ghent University [Belgium] (UGENT), CBS-KNAW Fungal Biodiversity Centre, University of California, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-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), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Georg-August-University = Georg-August-Universität Göttingen, Universiteit Gent = Ghent University (UGENT), and University of California (UC)

Subjects
0106 biological sciences, Species complex, Physiology, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Quantitative Trait Loci, Heterobasidion annosum, Plant Science, Quantitative trait locus, 01 natural sciences, Genome, HETEROBASIDION, Trees, 03 medical and health sciences, Botany, Forest ecology, medicine, SAPROTROPHY, Gene, WOOD DECAY, 030304 developmental biology, 0303 health sciences, biology, Heterobasidion irregulare, Basidiomycota, Gene Expression Profiling, Chromosome Mapping, 15. Life on land, biology.organism_classification, Wood, GENOME, medicine.drug_formulation_ingredient, PATHOLOGY, TRADE-OFF, Host-Pathogen Interactions, Genome, Fungal, Heterobasidion, PARASITISM, 010606 plant biology & botany
Abstract

International audience; Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato. We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified. A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production. Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.

Published
2012
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25. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

Author

Robin A. Ohm, Jianping Xu, Andrea Aerts, Taina Lundell, Andy M. Bailey, Robert Riley, Ronald P. de Vries, Annegret Kohler, Gary D. Foster, Pedro M. Coutinho, Vincent Lombard, David S. Hibbett, Kristiina Hildén, Aleksandrina Patyshakuliyeva, László Nagy, Michael P. Challen, Francis Martin, Jeremy Schmutz, Dan Cullen, Anton S.M. Sonnenberg, Han A. B. Wösten, Jane Grimwood, Venkataramanan Subramanian, Susan Lucas, Christophe Billette, Annick Brun, Harshavardhan Doddapaneni, Kerry S. Burton, Alla Lapidus, Richard W. Kerrigan, Bernard Henrissat, Claude Murat, Greg Deakin, Igor V. Grigoriev, Marie Foulongne-Oriol, Dimitrios Floudas, Kurt LaButti, Asaf Salamov, Ursula Kües, Emmanuelle Morin, Daniel C. Eastwood, Erika Lindquist, Adam Baker, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), University of Warwick [Coventry], Unité de recherche Mycologie et Sécurité des Aliments (MycSA), Institut National de la Recherche Agronomique (INRA), Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Clark University, United States Department of Energy, Utrecht University [Utrecht], Royal Netherlands Academy of Arts and Sciences (KNAW), University of Bristol [Bristol], East Malling Research, Department of Biology, Carver Center for Genomics, Iowa State University (ISU), University of Helsinki, Georg-August-University [Göttingen], Hudson Alpha Institute, Biosciences Center, National Renewable Energy Laboratory, McMaster University [Hamilton, Ontario], Swansea University, Wageningen University and Research [Wageningen] (WUR), Forest Products Laboratory, Centre National de la Recherche Scientifique (CNRS), Sylvan Biosciences, University of Oxford [Oxford], Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Georg-August-University = Georg-August-Universität Göttingen, University of Oxford, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Unité de recherche Mycologie et Sécurité des Aliments (MSA), and Wageningen University and Research Centre [Wageningen] (WUR)

Subjects
chromosomes, Agaricus, [SDV]Life Sciences [q-bio], Protein degradation, Lignin, complex mixtures, litter decay, Evolution, Molecular, substances, 03 medical and health sciences, litter decay wood, Laccaria bicolor, Botany, coprinus-cinereus, gene, Gene, decay fungi, Mycelium, 030304 developmental biology, degradation, 2. Zero hunger, 0303 health sciences, Mushroom, Multidisciplinary, decomposition, Ecology, biology, 030306 microbiology, humic substances, QK, fungi, schizophyllum-commune, Biological Sciences, 15. Life on land, biology.organism_classification, Adaptation, Physiological, Coprinopsis cinerea, Plant Breeding, carbohydrate-active enzymes, cultivated mushroom, Genome, Fungal, coprinopsis-cinerea, Agaricus bisporus, wood decay fungi
Abstract

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor . A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.

Published
2012
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26. The genome portal of the Department of Energy Joint Genome Institute

Author

Roman Nikitin, Igor Ratnere, Simon Minovitsky, Inna Dubchak, Igor V. Grigoriev, Alexander Poliakov, Henrik P. Nordberg, Andrea Aerts, Robert Riley, Daniel S. Rokhsar, David Goodstein, Robin A. Ohm, Alan Kuo, Tatyana Smirnova, Michael N. Cantor, Robert Otillar, and Igor Shabalov

Subjects
Genetics, Internet, business.industry, Data management, Genomic data, Genomics, Molecular Sequence Annotation, Sequence Analysis, DNA, Articles, Biology, Genome, DNA sequencing, World Wide Web, Systems Integration, Databases, Genetic, Cluster Analysis, Fungal genome, The Internet, Genome, Fungal, business, Software
Abstract

The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal (http://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. We describe here the general organization of the Genome Portal and the most recent addition, MycoCosm (http://jgi.doe.gov/fungi), a new integrated fungal genomics resource.

Published
2011

27. Obligate biotrophy features unraveled by the genomic analysis of rust fungi

Author

Richard C. Hamelin, Jacqueline E. Schein, Brandi L. Cantarel, Bernard Henrissat, Peter N. Dodds, Robert F. Park, Rohit Mago, Ursula Kües, Pedro M. Coutinho, Stéphane Hacquard, Joelle Amselem, Philippe Tanguay, Nicolas Feau, Claire Veneault-Fourrey, Annegret Kohler, Claude Murat, Chinnappa D. Kodira, Sébastien Duplessis, Erika Lindquist, Pierre Rouzé, Readman Chiu, Christina A. Cuomo, Emmanuelle Morin, Jonathan M. Goldberg, Nicolas Rouhier, Jasmyn Pangilinan, Manfred Grabherr, Yves Van de Peer, Matthew Pearson, Andrea Aerts, Igor V. Grigoriev, Susan Lucas, Shaobin Zhong, Benjamin Selles, Gerald A. Tuskan, Eric Gelhaye, Asaf Salamov, Jeremy Schmutz, Yao-Cheng Lin, Jeffrey G. Ellis, Harris Shapiro, Emilie Tisserant, David L. Joly, Sharadha Sakthikumar, Hadi Quesneville, Evan Mauceli, Matthew A. Field, Pascal Frey, Les J. Szabo, Francis Martin, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Institute of Massachuetts Institute of technology and harward university, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston]-Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Department of plant systems biology, Flanders Institute for Biotechnology, Joint Genome institute, United States Department of Energy, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Genome sciences, BC Cancer Agency (BCCRC), Division of molecular wood biotechnology and technical mycology - Büsgen-Institute, Bûsgenweg, Georg-August-Universität Göttingen, Plant Industry, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Plant breeding institute Cobbitty, The University of Sydney, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Department of plant pathology, University of Minnesota [Twin Cities], University of Minnesota System-University of Minnesota System, Cereal diseases laboratory US D epartment of agriculture, Agricultural Research Service, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Georg-August-University = Georg-August-Universität Göttingen, University of Minnesota [Twin Cities] (UMN), USDA-ARS : Agricultural Research Service, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Georg-August-University [Göttingen], Duplessis, Sébastien, Cuomo, Christina A, Szabo, Les J, and Martin, Francis

Subjects
puccinia graminis tritici, 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Rust (fungus), champignon phytopathogène, Stem rust, 01 natural sciences, Genome, Haustorium, Triticum, Phylogeny, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, biology, Sulfates, food and beverages, Melampsora, Biological Sciences, Plants, Adaptation, Physiological, rouille, melampsora larici populina, séquençage du génome, Genome, Fungal, RUST EVOLUTION, COMPARATIVE GENOMICS, Genes, Fungal, champignon biotrophique, Genes, Plant, Models, Biological, 03 medical and health sciences, PLANT PATHOGEN, BASIDIOMYCETE, EVOLUTION, Commentaries, Symbiosis, Plant Diseases, 030304 developmental biology, Comparative genomics, Puccinia, Nitrates, Models, Genetic, Obligate, Basidiomycota, Gene Expression Profiling, fungi, Fungi, Sequence Analysis, DNA, biology.organism_classification, Plant Leaves, Immune System, 010606 plant biology & botany
Abstract

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 cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101-Mb genome of Melampsora larici - populina , the causal agent of poplar leaf rust, and the 89-Mb genome of Puccinia graminis f. sp. tritici , the causal agent of wheat and barley stem rust. We then compared the 16,399 predicted proteins of M. larici-populina with the 17,773 predicted proteins of P. graminis f. sp tritici . Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells.

Published
2011
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28. The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

Author

Claude Murat, Kerrie Barry, Dirk Hoffmeister, Inger Skrede, Allen C. Gathman, Antonio G. Pisabarro, Dimitrios Floudas, Igor V. Grigoriev, Anna Rosling, Andrzej Majcherczyk, Jan Stenlid, Asaf Salamov, David S. Hibbett, José A. Oguiza, Katarina Ihrmark, Andrea Aerts, Xinfeng Xie, Walt W. Lilly, Manfred Binder, Francis Martin, Nils Högberg, Patrick Schneider, Barry Goodell, Dan Cullen, Annegret Kohler, Susan Lucas, Bernard Henrissat, Ad Wiebenga, Kurt LaButti, Mika Bendiksby, S.C. Watkinson, Ursula Kües, Scott E. Baker, Jeremy Schmutz, Erika Lindquist, Melanie Blumentritt, Daniel C. Eastwood, Olaf Schmidt, Jongsun Park, Fred O. Asiegbu, Emmanuelle Morin, Yong-Hwan Lee, Pedro M. Coutinho, José Luis Lavín, Håvard Kauserud, Robert Riley, Ronald P. de Vries, Alla Lapidus, Swansea University, Clark University, Busgen Inst, Georg-August-University = Georg-August-Universität Göttingen, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], United States Department of Energy, Dept Forest Sci, ESALQ USP, Joint Genome Inst, Pacific Northwest National Laboratory (PNNL), Natural History Museum [Oslo], University of Oslo (UiO), University of Maine, Université de Provence - Aix-Marseille 1, Université de la Méditerranée - Aix-Marseille 2, Forest Prod Lab, United States Department of Agriculture, Royal Netherlands Academy of Arts and Sciences (KNAW), Southeast Missouri State University, Virginia Polytechnic Institute and State University [Blacksburg], Swedish University of Agricultural Sciences (SLU), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Universidad de Navarra [Pamplona] (UNAV), Seoul National University [Seoul] (SNU), University of Hamburg, University of Oxford, Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231], Georg-August-University [Göttingen], and University of Oxford [Oxford]

Subjects
LITTER, Proteome, [SDV]Life Sciences [q-bio], WOOD, Lignin, Trees, chemistry.chemical_compound, Cell Wall, Mycorrhizae, Phylogeny, 0303 health sciences, Multidisciplinary, biology, Ecology, SYMBIOSIS, food and beverages, Biota, Basidiomycota, Biodiversity, Genomics, Biological Evolution, GENOME, Peroxidases, DIVERSIFICATION, Oxidoreductases, Serpula lacrymans, Genes, Fungal, Fungus, macromolecular substances, SERPULA-LACRYMANS, complex mixtures, MECHANISMS, Cell wall, 03 medical and health sciences, Magnoliopsida, Symbiosis, Botany, 030304 developmental biology, 030306 microbiology, Gene Expression Profiling, technology, industry, and agriculture, 15. Life on land, biology.organism_classification, DECAY FUNGI, Tracheophyta, CONVERSION, chemistry, Dry rot, Coriolaceae
Abstract

International audience; Brown rot decay removes cellulose and hemicellulose from wood-residual lignin contributing up to 30% of forest soil carbon-and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.

Published
2011
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29. Genome sequence of the model mushroom Schizophyllum commune

Author

Pedro M. Coutinho, Vincent Lombard, Jon K. Magnuson, Eric Record, Francis W. M. R. Schwarze, Andrea Aerts, Susann Erdmann, Erika Lindquist, J. Stephen Horton, Bernard Henrissat, Nicole Knabe, Erika Kothe, Igor V. Grigoriev, Susan Lucas, Walt W. Lilly, Robin A. Ohm, Marjatta Raudaskoski, Kirk A Bartholomew, Jason E. Stajich, Thomas J. Fowler, François Piumi, Scott E. Baker, Ronald P. de Vries, Jan F. de Jong, Ursula Kües, Patricia A. vanKuyk, Luis G. Lugones, Jeremy Schmutz, Asaf Salamov, Han A. B. Wösten, Anthony Levasseur, Allen C. Gathman, Unité mixte de recherche de biotechnologie des champignons filamenteux, and Université de la Méditerranée - Aix-Marseille 2-Institut National de la Recherche Agronomique (INRA)-Université de Provence - Aix-Marseille 1

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, animal structures, Biomedical Engineering, Bioengineering, Fungus, Schizophyllum, Applied Microbiology and Biotechnology, Genome, Models, Biological, Neurospora crassa, Fungal Proteins, 03 medical and health sciences, Gene Expression Regulation, Plant, Fruiting Bodies, Fungal, Gene, 030304 developmental biology, Genetics, 0303 health sciences, Mushroom, biology, Base Sequence, 030306 microbiology, Gene Expression Profiling, fungi, Schizophyllum commune, Fungal genetics, food and beverages, Gene Expression Regulation, Developmental, Basidiomycota, biology.organism_classification, Genes, Mating Type, Fungal, Wood, Genetic Loci, Molecular Medicine, Genome, Fungal, Biotechnology, Transcription Factors
Abstract

Much remains to be learned about the biology of mushroom-forming fungi, which are an important source of food, secondary metabolites and industrial enzymes. The wood-degrading fungus Schizophyllum commune is both a genetically tractable model for studying mushroom development and a likely source of enzymes capable of efficient degradation of lignocellulosic biomass. Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune. Whereas inactivation of one of these, fst4, prevented mushroom formation, inactivation of another, fst3, resulted in more, albeit smaller, mushrooms than in the wild-type fungus. Antisense transcripts may also have a role in the formation of fruiting bodies. Better insight into the mechanisms underlying mushroom formation should affect commercial production of mushrooms and their industrial use for producing enzymes and pharmaceuticals.

Published
2010
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30. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Author

Evelyne Derelle, Jeremy Schmutz, Carolyn A. Napoli, Andrea L Manuell, Marc Heijde, Asaf Salamov, Robert Otillar, Séverine Jancek, Hervé Moreau, Stephane Rombauts, Karla C Gendler, Gwenael Piganeau, Charles F. Delwiche, Olivier Vallon, Qinghu Ren, Gregory Werner, Igor V. Grigoriev, Jane Grimwood, Ian T. Paulsen, Daniel S. Rokhsar, Martin Lohr, Gregory J. Pazour, Terry Gaasterland, Sabeeha S. Merchant, Pierre Rouzé, Steven Robbens, Kamel Jabbari, Christopher L. Dupont, Chris Bowler, Richard A. Jorgensen, Brian Palenik, Sheila Podell, Andrea Aerts, Kemin Zhou, Vera Tai, Inna Dubchak, Yves Van de Peer, Nicholas H. Putnam, Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Genome evolution, Protein family, Gene Transfer, Horizontal, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Biology, Environment, 01 natural sciences, Genome, Chromosomes, Ostreococcus tauri, Ostreococcus, 03 medical and health sciences, Chlorophyta, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Selenoproteins, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, Cell Nucleus, 0303 health sciences, Multidisciplinary, Metal metabolism, Vitamins, Biological Sciences, biology.organism_classification, Plankton, Adaptation, Physiological, Biological Evolution, Eukaryotic Cells, Metals, Horizontal gene transfer, 010606 plant biology & botany
Abstract

The smallest known eukaryotes, at ≈1-μm diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri . This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.

Published
2007
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31. Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis

Author

Harris Shapiro, Andrea Aerts, Yong Su Jin, Igor V. Grigoriev, Thomas W. Jeffries, Asaf Salamov, Volkmar Passoth, Paul G. Richardson, Jeremy Schmutz, Jane Grimwood, Jose M. Laplaza, Erika Lindquist, and Paramvir S. Dehal

Subjects
Sequence analysis, Bioconversion, Saccharomyces cerevisiae, Molecular Sequence Data, Biomedical Engineering, Bioengineering, Xylose, Applied Microbiology and Biotechnology, Genome, Lignin, Pichia, chemistry.chemical_compound, Xylose metabolism, Biomass, Pichia stipitis, Cellulose, DNA, Fungal, Phylogeny, Gene Library, biology, food and beverages, Sequence Analysis, DNA, biology.organism_classification, Yeast, Biosynthetic Pathways, chemistry, Biochemistry, Fermentation, Molecular Medicine, Sequence Alignment, Genome, Bacterial, Biotechnology
Abstract

Xylose is a major constituent of plant lignocellulose, and its fermentation is important for the bioconversion of plant biomass to fuels and chemicals. Pichia stipitis is a well-studied, native xylose-fermenting yeast. The mechanism and regulation of xylose metabolism in P. stipitis have been characterized and genes from P. stipitis have been used to engineer xylose metabolism in Saccharomyces cerevisiae. We have sequenced and assembled the complete genome of P. stipitis. The sequence data have revealed unusual aspects of genome organization, numerous genes for bioconversion, a preliminary insight into regulation of central metabolic pathways and several examples of colocalized genes with related functions. The genome sequence provides insight into how P. stipitis regulates its redox balance while very efficiently fermenting xylose under microaerobic conditions.

Published
2006

32. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis

Author

Bruno W. S. Sobral, Mark Gijzen, Alon Savidor, Brett M. Tyler, Sam Rash, Francine Govers, Rays H. Y. Jiang, Paul Morris, Mi-Kyung Lee, Kurt Lamour, Anne E. Dorrance, Sucheta Tripathy, C. M. B. Damasceno, Donald J. Maclean, Richard W. Jones, Matteo Garbelotto, Sophien Kamoun, Yasuko Sakihama, Daniel S. Rokhsar, Trudy Torto-Alalibo, Stuart G. Gordon, MoÌnica Medina, Jocelyn K. C. Rose, Daolong Dou, Astrid Terry, Harold J. G. Meijer, Hong-Bin Zhang, Brian M. Smith, Zhanyou Xu, Igor V. Grigoriev, Konstantinos Krampis, Eric K. Nordberg, Niklaus J. Grünwald, Jim Beynon, Vipaporn Phuntumart, Laura Baxter, Felipe D. Arredondo, Chantel F. Scheuring, Andrea Aerts, Jarrod Chapman, Wayne Huang, W. Hayes McDonald, Paramvir S. Dehal, Joe Win, Inna Dubchak, Manuel D. Ospina-Giraldo, Douda Bensasson, Asaf Salamov, Nicholas H. Putnam, Allan W. Dickerman, Kelly Ivors, Jeffrey L. Boore, and Xuemin Zhang

Subjects
Phytophthora, Protein family, Sequence analysis, Hydrolases, effector proteins, Genome, avirulence, Polymorphism, Single Nucleotide, resistance, DNA, Algal, Phylogenetics, Phytophthora ramorum, Botany, expression, Phytophthora sojae, Photosynthesis, genes, Symbiosis, Phylogeny, Plant Diseases, Repetitive Sequences, Nucleic Acid, Toxins, Biological, Genetics, Oomycete, locus, Multidisciplinary, biology, EPS-2, downy mildew, fungi, Algal Proteins, food and beverages, Sequence Analysis, DNA, biology.organism_classification, Physical Chromosome Mapping, Biological Evolution, Laboratorium voor Phytopathologie, virulence, arabidopsis, Genes, Laboratory of Phytopathology, sojae
Abstract

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum . Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.

Published
2006

33. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Author

Jérémy Couturier, Astrid Terry, Annabelle Déjardin, Kaisa Nieminen, Chandrashekhar P. Joshi, Wenyu Huang, G.-L. Chen, D. Holligan, Richard A. Jorgensen, Gilles Pilate, Paul G. Richardson, John C. Detter, Uffe Hellsten, Asim Siddiqui, J. Razumovskaya, T. Yin, Francis Martin, Per Unneberg, V. Pereda, Rishikeshi Bhalerao, Carolyn A. Napoli, Jorma Vahala, Jim Leebens-Mack, R. Cunningham, Matias Kirst, Inna Dubchak, Victor Busov, Fredrik Sterky, Daniel S. Rokhsar, Andrew Groover, Sven Degroeve, Marco A. Marra, Alexander Poliakov, Stephane Rombauts, D. Ryaboy, Jean-Charles Leplé, Jaakko Kangasjärvi, Lieven Sterck, Kerr Wall, Pierre Rouzé, Jane Grimwood, N. Islam-Faridi, Michael Gribskov, Jeremy Schmutz, Björn Hamberger, Bo Segerman, Robert Kirkpatrick, Joerg Bohlmann, Damien Blaudez, David R. Nelson, Stefan Jansson, Y. Van de Peer, Sébastien Duplessis, Cécile Rinaldi, Brian E. Ellis, Amy M. Brunner, Robert A. Holt, Chung-Jui Tsai, Sarah F. Covert, Pedro M. Coutinho, Edward C. Uberbacher, Guojun Yang, M. Jones-Rhoades, Udaya C. Kalluri, Carl J. Douglas, J. Schrader, Kermit Ritland, C D Nelson, Bernard Henrissat, Andrea Aerts, Igor V. Grigoriev, Susan R. Wessler, Gerald A. Tuskan, Steven J.M. Jones, Philip F. LoCascio, Barbara Montanini, Yrjö Helariutta, Jacquie Schein, Quentin C. B. Cronk, Lee E. Gunter, H. Shin, Ryan N. Philippe, Ove Nilsson, Göran Sandberg, Susan Lucas, Nicholas H. Putnam, Berthold Heinze, Karla C Gendler, John E. Carlson, Jan Karlsson, Jarrod Chapman, Stephen P. DiFazio, Michel Chalot, Gary F. Peter, Steven G. Ralph, Dawn Cooper, Colin T. Kelleher, Malcolm M. Campbell, Annegret Kohler, Frank W. Larimer, Bill Dirks, Rishikesh P. Bhalerao, John M. Davis, Wout Boerjan, Jürgen Ehlting, Y. Lou, David Goodstein, Annick Brun, Asaf Salamov, Claude W. dePamphilis, Environmental Sciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, University of Tennessee, Department of Biology, West Virginia University, Swedish University of Agricultural Sciences (SLU), Michael Smith Laboratories, University of British Columbia (UBC), Joint Genome Institute (JGI), Department of plant systems biology, Flanders Institute for Biotechnology, Canada's Michael Smith Genome Sciences Centre (CMSGSC), BC Cancer Agency (BCCRC), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Virginia Polytechnic Institute and State University [Blacksburg], Michigan Technological University (MTU), Department of Cell and Systems Biology, University of Toronto, Pennsylvania State University (Penn State), Penn State System, Oak Ridge National Laboratory, Université de la Méditerranée - Aix-Marseille 2, Warnell School of Forest Resources, Department of Botany, University of Florida [Gainesville] (UF), Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), University of California [Berkeley], University of California, Genomics Division [LBNL Berkeley], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), University of Arizona, Department of Biological Sciences [Lafayette IN], Purdue University [West Lafayette], Stanford University, US Forest Service, Federal Research and Training Centre for Forests Natural Hazards and Landscape, University of Helsinki, Northern Arizona University [Flagstaff], Department of Plant Biology, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), United States Department of Agriculture, Texas A&M University System, Whitehead Institute for Biomedical Research and Department of Biology (MIT), Massachusetts Institute of Technology (MIT), Department of Molecular Sciences and Center of Excellence in Genomics and Bioinformatics, The University of Tennessee [Knoxville], Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Department of Forest Sciences [Vancouver], Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Royal Institute of Technology in Stockholm (KTH), University of California [Berkeley] (UC Berkeley), University of California (UC), and Helsingin yliopisto = Helsingfors universitet = University of Helsinki

Subjects
0106 biological sciences, Populus trichocarpa, RNA, Untranslated, POPULUS TRICHOCARPA, IDENTIFICATION DE GENES, Arabidopsis, Gene Expression, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Genes, Plant, 01 natural sciences, Genome, Polymorphism, Single Nucleotide, Evolution, Molecular, 03 medical and health sciences, Gene mapping, Gene Duplication, Gene, Populus balsamifera, Phylogeny, 030304 developmental biology, Genomic organization, Oligonucleotide Array Sequence Analysis, Plant Proteins, Genetics, Expressed Sequence Tags, 0303 health sciences, Multidisciplinary, biology, fungi, Chromosome Mapping, Computational Biology, Sequence Analysis, DNA, biology.organism_classification, Protein Structure, Tertiary, Paleopolyploidy, Populus, RNA, Plant, PEUPLIER, Genome, Plant, 010606 plant biology & botany
Abstract

We report the draft genome of the black cottonwood tree, Populus trichocarpa . Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis , ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Published
2006
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34. Genome sequences of two Phytophthora species responsible for Sudden Oak Death and Soybean Root Rot provide novel insights into their evolutionary origins and mechanisms of pathogenesis

Author

Douda Bensasson, Nik Putnam, Hayes McDonald, Andrea Aerts, Jeffrey L. Boore, Asaf Salamov, Wayne Huang, Paul G. Morris, Konstantinos Krampis, Sophien Kamoun, Sucheta Tripathi, Matteo Garbelotto, Rays H. Y. Jiang, Kurt Lamour, Igor V. Grigoriev, Inna Dubchak, Brian M. Smith, Joseph E. Smith, Daniel S. Rokhsar, Paramvir S. Dehal, Kelly Ivors, Trudy A. Torto, Astrid Terry, Mónica Medina, Mark Gijzen, Brett M. Tyler, and Sam Rash

Subjects
Blowing a raspberry, Horticulture, Perennial plant, Agronomy, Host (biology), Range (biology), Ornamental plant, Root rot, Famine, Phytophthora, Biology, biology.organism_classification
Abstract

The approximately 60 species of Phytophthora are all destructive pathogens, causing rots of roots, stems, leaves and fruits of a wide range of agriculturally and ornamentally important plants (1). Some species, such as P. cinnamomi, P. parasitica and P. cactorum, each attack hundreds of different plant host species, whereas others are more restricted. Some of the crops where Phytophthora infections cause the greatest financial losses include potato, soybean, tomato, alfalfa, tobacco, peppers, cucurbits, pineapple, strawberry, raspberry and a wide range of perennial tree crops, especially citrus, avocado, almonds, walnuts, apples and cocoa, and they also heavily affect the ornamental, nursery and forestry industries. The economic damage overall to crops in the United States by Phytophthora species is estimated in the tens of billions of dollars, including the costs of control measures, and worldwide it is many times this amount (1). In the northern midwest of the U.S., P. sojae causes $200 million in annual losses to soybean alone, and worldwide causes around $1-2 billion in losses per year. P. infestans infections resulted in the Irish potato famine last century and continues to be a difficult and worsening problem for potato and tomato growers worldwide, with worldwide costs estimated at $5more » billion per year.« less

Published
2005
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35. Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins

Author

Patrick Minges, Nik Putnam, Jill Gaskell, Dan Cullen, Igor V. Grigoriev, Phil Kersten, Paula Belinky, Harris Shapiro, Amber Vanden Wymelenberg, Carlos G. Dosoretz, Grzegorz Sabat, Andrea Aerts, Diego Martinez, and Asaf Salamov

Subjects
Glycoside Hydrolases, Hypothetical protein, Phanerochaete, Microbiology, Mass Spectrometry, Fungal Proteins, Gene cluster, Genetics, Gene family, Glycoside hydrolase, Gene, biology, Sequence Homology, Amino Acid, Computational Biology, Lignin peroxidase, Lipase, biology.organism_classification, Phosphoric Monoester Hydrolases, Culture Media, Protein Transport, Biochemistry, Peroxidases, Proteome, Genome, Fungal, Databases, Nucleic Acid, Carboxylic Ester Hydrolases, Peptide Hydrolases
Abstract

The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identiWed in the earlier database (v1.0). Within the v2.1 ‘computational secretome,’ 43% showed no signiWcant similarity to known proteins, but were structurally related to other hypothetical protein sequences. In contrast, 53% showed signiWcant similarity to known protein sequences including 87 models assigned to 33 glycoside hydrolase families and 52 sequences distributed among 13 peptidase families. When grown under standard ligninolytic conditions, peptides corresponding to 11 peptidase genes were identiWed in culture Wltrates by mass spectrometry (LS–MS/MS). Five peptidases were members of a large family of aspartyl proteases, many of which were localized to gene clusters. Consistent with a role in dephosphorylation of lignin peroxidase, a mannose-6-phosphatase (M6Pase) was also identiWed in carbon-starved cultures. Beyond proteases and M6Pase, 28 speciWc gene products were identiWed including several representatives of gene families. These included 4 lignin peroxidases, 3 lipases, 2 carboxylesterases, and 8 glycosyl hydrolases. The results underscore the rich genetic diversity and complexity of P. chrysosporium’s extracellular enzyme systems. Published by Elsevier Inc.

Published
2005

36. A genetic variation map for chicken with 2.8 million single nucleotide polymorphisms

Author

Dong Wei, James C. Kaufman, Bailin Hao, Heng Li, Susan Lucas, Henk Bovenhuis, Fengdi Lan, Jun Yu, Dirk-Jan de Koning, Wei-Mou Zheng, Pei Wang, Guoqing Li, Stuart A. Wilson, Xu Yang, Qingshun Meng, Hongkun Zheng, Jianping Shi, Bin Liu, Nat Bumstead, Ivan Ovcharenko, Mingtao Dai, Lisa Stubbs, Andrea Aerts, Yan Zhou, Hans H. Cheng, Miaoheng Wang, Per Wahlberg, Jian Wang, Andy van Hateren, Neil Bartley, Wenming Zhao, Wenjie Li, Paul E. Boardman, Xiaoling Wang, Hans Ellegren, Le Dong, Jia Ye, Paul M Hocking, Zheng Yang, Henry D. Hunt, Susan J. Lamont, Chen Ye, Jing Wang, Xiaowei Zhang, Guangyuan Li, Dawei Li, David W. Burt, Björn Andersson, Ximiao He, Simon J. Hubbard, Yanqing Huang, Ian M. Overton, Jingjing Zhang, Longhua Ran, Jun Wang, Peter K. Kaiser, Ning Li, Zengjin Zhang, Yingpu Yu, Martien A. M. Groenen, Andy Law, Fei Xie, Shiaw Pyng Yang, Jue Ruan, Chris P. Ponting, LaDeana W. Hillier, Huanming Yang, Songgang Li, Changqing Zeng, John R. Young, Martti T. Tammi, Wei Lin, Sally L. Rogers, Peixiang Ni, Huaijun Zhou, Ning Yang, Ruiqiang Li, Yongqiao Sun, Yuanzhe Li, Ellen Kindlund, Ning Wei, Chen Chen, Jun Zhou, Xiangang Huang, Yunze Zhang, Richard P. M. A. Crooijmans, Wei Dong, Songnian Hu, Yan Xi, Gane Ka-Shu Wong, Ulrika Gunnarsson, Tijana Glavina, Yiqiang Zhao, Mikael Brandström, Jun Li, Yong Zhang, Leif Andersson, Jan J. van der Poel, Jie Chen, Lisa Rothwell, Caleb Webber, Haizhou Tang, Jianjun Wang, Brian A Walker, Zhenpeng Zhang, Laurie Gordon, Jianguo Zhang, Shengting Li, David R. Morrice, Dandan He, Wei Tong, Qiuhui Qi, Wesley C. Warren, and Richard K. Wilson

Subjects
Genetics, Multidisciplinary, Haplotype, Genetic variation, Single-nucleotide polymorphism, Genomics, Allele, Biology, Quantitative trait locus, Domestication, Article, Nucleotide diversity
Abstract

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.

Published
2004
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37. The sequence and analysis of duplication-rich human chromosome 16

Author

Kimberly L. Mcmurray, James Retterer, Nancy C. Brown, Dea Fotopulos, Michael R. Altherr, Judith G. Tesmer, Jane Grimwood, Joel Martin, Jonathan L. Longmire, Elizabeth Saunders, P. Scott White, Malinda Stalvey, Elbert Branscomb, Norman A. Doggett, Nina Thayer, C.E. Hildebrand, Mary Bao Tran-Gyamfi, Yunian Lou, Trevor Hawkins, Lucía Ramírez, Shyam Prabhakar, Ming Tsai, D. Scott, Hope Tice, Linda Meincke, Jean F. Challacombe, Gary Xie, Maria Gomez, Eidelyn Gonzales, Jeremy Schmutz, Kevin Wu, Marie-Claude Krawczyk, Heather Kimball, Graham A. Mark, David C. Torney, John C. Detter, Laurie Gordon, Albert L. Williams, Susan Lucas, Len A. Pennacchio, Linda S. Thompson, Robert K. Moyzis, Kristen Kadner, Arthur Kobayashi, Larry L. Deaven, Richard D. Nandkeshwar, E.W. Campbell, Patricia L. Wills, Andrea Aerts, Joan Yang, Darryl O. Ricke, Mark Dickson, Astrid Terry, Steve Lowry, Paul Gilna, Paul G. Richardson, Thom Ludeman, Olivier Couronne, Timothy Shough, Chitra Manohar, David Bruce, Jamie Jett, Evan E. Eichler, Pieter J. deJong, Mark Mundt, Judith M. Buckingham, Robert D. Sutherland, Roxanne Tapia, Heather Blumer, Wayne Huang, Leslie Chasteen, A. Christine Munk, Sanjay Israni, Deborah L. Grady, Igor V. Grigoriev, Stacey Black, Judith D. Cohn, David F. Callen, Han C. Chi, William J. Bruno, Cliff Han, Mirian Denys, Mira Dimitrijevic-Bussod, Martin Pollard, Connie S. Campbell, Richard M. Myers, Yee Man Chan, Sam Pitluck, Sam Rash, Joseph J. Fawcett, Mari Christensen, Lauren Haydu, Frederick Lopez, Lynn M. Clark, Julio Escobar, B. Parson-Quintana, Raymond L. Stallings, Tina Leyba, Dave Flowers, Eva Bajorek, Jenna Morgan, Mary L. Campbell, Anna Ustaszewska, Donna L. Robinson, Nu Vo, Edward M. Rubin, Lynne Goodwin, Paul Predki, Uffe Hellsten, Daniel S. Rokhsar, Phillip B. Jewett, Matthew Groza, Tijana Glavina, Chenier Caoile, Alex Rodriguez, Xinwei She, David Goodstein, Jung-Rung Wu, Levy E. Ulanovsky, Asaf Salamov, Nancy Hammon, and Olga Chertkov

Subjects
Genetics, Multidisciplinary, Autosome, Polymorphism, Genetic, Sequence analysis, Pseudogene, Molecular Sequence Data, Genomics, Sequence Analysis, DNA, Biology, Physical Chromosome Mapping, Synteny, Chromosome 16, Genes, Gene Duplication, Heterochromatin, Gene duplication, Gene family, Animals, Humans, Gene, Chromosomes, Human, Pair 16, Segmental duplication
Abstract

Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.

Published
2004

38. The DNA sequence and biology of human chromosome 19

Author

Mary Bao Tran-Gyamfi, Ivan Ovcharenko, Trevor Hawkins, Maria Gomez, Mirian Denys, Victor V. Solovyev, Terrence S. Furey, Jamie Jett, Jeremy Schmutz, Dea Fotopulos, David Gordon, Tom Slezak, Kevin Wu, Heather Kimball, Pieter J. deJong, Catherine Medina, Vladimer Larionov, Paula McCready, Stephanine Rogers, James Retterer, John C. Detter, Diego Martinez, Richard M. Myers, Paul Predki, Stacey Black, Eva Bajorek, Chenier Caoile, Alex Rodriguez, Isaac Ho, Arthur Kobayashi, Jane Lamerdin, Xinwei She, Yunian Lou, Jane Grimwood, Kristen Kadner, Alex Copeland, Wayne Huang, Sanjay Israni, Carmen Rosa Albacete García, Gary Xie, Doug Smith, Anthony V. Carrano, Matthew Groza, Catherine A. Cleland, Matt Nolan, Paul G. Richardson, Eidelyn Gonzales, Nina Thayer, Anna Ustaszewska, Eileen Dalin, Olivier Couronne, Evan E. Eichler, Tijana Glavina, Astrid Terry, Sun-Hee Leem, Steve Lowry, Anne S. Olsen, Lucía Ramírez, Ming Tsai, Stephanie Malfatti, Hope Tice, Uffe Hellsten, David Goodstein, Martin Pollard, Daniel S. Rokhsar, Nancy Hammon, Angelica Salazar, Jenna Morgan, Yee Man Chan, Michael R. Altherr, Paramvir S. Dehal, Nu Vo, Linda K. Ashworth, Elbert Branscomb, Laurie Gordon, Julio Escobar, Anthony P. Popkie, Dave Flowers, Anca M. Georgescu, Len A. Pennacchio, Sam Pitluck, Sam Rash, Edward M. Rubin, Sean Caenepeel, Glenda Quan, Asaf Salamov, Inna Dubchak, Lisa Stubbs, Andrea Aerts, Mark Dickson, Kathryn Nelson, Mari Christensen, Lauren Haydu, Frederick Lopez, Mark C. Wagner, Jeremy Wheeler, Joan Yang, and Susan Lucas

Subjects
Genetics, Medical, Molecular Sequence Data, Biology, Evolution, Molecular, Chromosome 15, Mice, Chromosome 16, Chromosome 19, Gene Duplication, Animals, Humans, Conserved Sequence, Genetics, Base Composition, Multidisciplinary, Sequence Analysis, DNA, Physical Chromosome Mapping, Chromosome 17 (human), Alternative Splicing, Chromosome 4, Chromosome 3, Genes, Multigene Family, CpG Islands, Chromosome 21, Chromosome 22, Chromosomes, Human, Pair 19, Pseudogenes
Abstract

Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.

Published
2003

39. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

Author

Sergio Casas-Flores, Stéphane Le Crom, Miguel Ángel Hernández-Oñate, Michael R. Thon, Nicolle H. Packer, Mette Lübeck, Andrea Aerts, Fabian Glaser, Elida Yazmin Gomez-Rodriguez, Monika Schmoll, Prasun K. Mukherjee, Mayte G Cervantes-Badillo, Michel Flipphi, Cliff Han, Erika Lindquist, Hans von Döhren, László Kredics, Alfredo Herrera-Estrella, Markus Omann, Diego Martinez, Zsuzsanna Antal, Edgardo Ulises Esquivel-Naranjo, Erzsébet Fekete, Luis David Alcaraz, Susan Lucas, Rosa Hermosa, Asaf Salamov, Monica Misra, Irina S. Druzhinina, Daniel J. Ebbole, Olga Chertkov, Enrique Monte, Aric Wiest, Fanny Coulpier, Mala Mukherjee, Christian P. Kubicek, Lea Atanasova, Nandan P. Deshpande, Harris Shapiro, Antoine Margeot, Jean F. Challacombe, Scott E. Baker, Edith Elena Uresti-Rivera, Doris Tisch, Bernhard Seiboth, Susanne Zeilinger, Levente Karaffa, Michael Zhang, Giancarlo Perrone, Idit Kosti, Igor V. Grigoriev, Juan Antonio Tamayo-Ramos, Verena Seidl-Seiboth, Benjamin Metz, Benjamin A. Horwitz, Sabine Gruber, Serenella A. Sukno, Peter Stephensen Lübeck, Helena Nevalainen, Heather H. Wilkinson, Kevin McCluskey, Charles M. Kenerley, Bernard Henrissat, Pedro M. Coutinho, Massachusetts Institute of Technology (MIT), Universidad de Salamanca, Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICYT), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Technion - Israel Institute of Technology [Haifa], University of Szeged [Szeged], DOE Joint Genome Institute [Walnut Creek], Los Alamos National Laboratory (LANL), University of Missouri [Kansas City] (UMKC), University of Missouri System, GenomiqueENS (Genomique ENS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Macquarie University, Texas A&M University System, Department of Energy / Joint Genome Institute (DOE), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aalborg University [Denmark] (AAU), IFP Energies nouvelles (IFPEN), Joint Genome Institute (JGI), United States Department of Energy, Institute of Sciences of Food Production (ISPA), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Vienna University of Technology (TU Wien), Wageningen University and Research [Wageningen] (WUR), Texas A&M University [College Station], United States Department of Energy (DOE) DE-AC02-05CH112Junta de Castilla y Leon GR67 Spanish GovernmentAustrian Science Fund (FWF)FWF P17895-B06 P20559 T390 P18109-B12 P-19421 V139B20 P-19340 Ramon y Cajal from the Spanish Ministry of Science and Innovation (MCINN) RYC-2004-003005 Vienna Science and Technology Fund WWTF LS09-036Austrian Science Fund (FWF) V 139, ANR-07-BIOE-0006,E-TRICEL,Exploration de la biodiversité enzymatique pour la complémentation du secrétome de Trichoderma reesei afin d'améliorer l'hydrolyse des lignocelluloses(2007), European Project: 13431-C02,AGL2009-13431-C02, European Project: 0512/AGR,AGL, Plateforme Génomique de l'IBENS, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Consiglio Nazionale delle Ricerche (CNR), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Sequence Analysis, DNA, MESH: Plants, eukaryotic genomes, Biológiai tudományok, Genome, aspergillus-nidulans, pathogenic fungi, MESH: Hypocrea, Természettudományok, Hypocrea, MESH: Pest Control, Biological, Systems and Synthetic Biology, MESH: Phylogeny, Phylogeny, Trichoderma reesei, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Trichoderma, 0303 health sciences, Systeem en Synthetische Biologie, neurospora-crassa, biology, Phylogenetic tree, Chromosome Mapping, food and beverages, Plants, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], cell-wall, MESH: DNA Transposable Elements, induced systemic resistance, MESH: Genome, Fungal, Genome, Fungal, dna-sequences, Fungus, 03 medical and health sciences, Species Specificity, Aspergillus nidulans, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, MESH: Species Specificity, Pest Control, Biological, 030304 developmental biology, VLAG, 030306 microbiology, Research, hypocrea-jecorina, Sequence Analysis, DNA, plant-root colonization, biology.organism_classification, MESH: Trichoderma, hydrophobin gene, DNA Transposable Elements, Mobile genetic elements, MESH: Chromosome Mapping
Abstract

Background Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. Results Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei. Conclusions The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.

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40. Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

Author

Bernard Henrissat, Radhakrishnan Mahadevan, Kerrie Barry, Alla Lapidus, Andrea Aerts, Pedro M. Coutinho, Patricia A. vanKuyk, Kiyohiko Igarashi, Masahiro Samejima, Mamdouh Abou-Zaid, Asaf Salamov, Susan Lucas, Khajamohiddin Syed, Hitoshi Suzuki, Igor V. Grigoriev, Chiaki Hori, Jacqueline MacDonald, Yunchen Gong, Ronald P. de Vries, Erika Lindquist, Jagjit S. Yadav, Ad Wiebenga, Kurt LaButti, and Emma R. Master

Subjects
Glycoside Hydrolases, lcsh:QH426-470, lcsh:Biotechnology, Phanerochaete chrysosporium, Phanerochaete, Fungal Proteins, Polyporaceae, Manganese peroxidase, softwood degradation, lcsh:TP248.13-248.65, Botany, Genetics, Phanerochaete carnosa, Chrysosporium, Fungal protein, biology, Comparative genomics, Fungal genetics, Genomics, biology.organism_classification, Wood, Metabolic pathway, lcsh:Genetics, Genome, Fungal, Softwood degradation, Research Article, Biotechnology
Abstract

Background Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome. Results P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood. Conclusions The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.

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