Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses.

Autor: Steindorff AS; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Aguilar-Pontes MV; Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada.; Departamento de Genética, University of Córdoba, 14071, Córdoba, Spain., Robinson AJ; Los Alamos National Laboratory, Los Alamos, NM, USA., Andreopoulos B; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., LaButti K; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Kuo A; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Mondo S; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Riley R; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Otillar R; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Haridas S; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Lipzen A; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Grimwood J; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA., Schmutz J; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA., Clum A; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; National Microbiome Data Collaborative, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Reid ID; Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada., Moisan MC; Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada., Butler G; Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada., Nguyen TTM; Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada., Dewar K; Department of Human Genetics, McGill University, Montreal, QC, Canada., Conant G; Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA., Drula E; Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, Marseille, France., Henrissat B; DTU Bioengineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark., Hansel C; Woods Hole Oceanographic Institution, Falmouth, MA, USA., Singer S; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Hutchinson MI; Department of Biology, The University of New Mexico, Albuquerque, NM, USA., de Vries RP; Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands., Natvig DO; Department of Biology, The University of New Mexico, Albuquerque, NM, USA., Powell AJ; Systems Design and Architecture, Sandia National Laboratories, Albuquerque, NM, 87123, USA., Tsang A; Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada., Grigoriev IV; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. ivgrigoriev@lbl.gov.; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA. ivgrigoriev@lbl.gov.

Publikováno v: Communications biology [Commun Biol] 2024 Sep 12; Vol. 7 (1), pp. 1124. Date of Electronic Publication: 2024 Sep 12.

Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces.

Autor: Barros KO; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.; Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.; Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil., Mader M; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA., Krause DJ; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.; Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA., Pangilinan J; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Andreopoulos B; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Department of Computer Science, San Jose State University, One Washington Square, San Jose, CA, USA., Lipzen A; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Mondo SJ; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Grigoriev IV; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Plant and Microbial Department, University of California Berkeley, Berkeley, CA, USA., Rosa CA; Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil., Sato TK; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA. tksato@glbrc.wisc.edu., Hittinger CT; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA. cthittinger@wisc.edu.; Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA. cthittinger@wisc.edu.

Publikováno v: Biotechnology for biofuels and bioproducts [Biotechnol Biofuels Bioprod] 2024 Feb 07; Vol. 17 (1), pp. 20. Date of Electronic Publication: 2024 Feb 07.

Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria.

Autor: Sahu N; Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary.; Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary., Indic B; Functional Genomics and Bioinformatics Group, Faculty of Forestry, Institute of Forest and Natural Resource Management, University of Sopron, Sopron, Hungary., Wong-Bajracharya J; Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia.; Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia., Merényi Z; Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary., Ke HM; Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.; Department of Microbiology, Soochow University, Taipei, Taiwan., Ahrendt S; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Monk TL; Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia., Kocsubé S; Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.; ELKH-SZTE Fungal Pathogenicity Mechanisms Research Group, University of Szeged, Szeged, Hungary., Drula E; Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France.; INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques, Marseille, France., Lipzen A; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Bálint B; Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary., Henrissat B; DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia., Andreopoulos B; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Martin FM; Université de Lorraine, INRAE, UMR 1136 'Interactions Arbres/Microorganismes', Centre INRAE Grand Est - Nancy, Champenoux, France., Bugge Harder C; Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, København Ø, Denmark.; Department of Biosciences, University of Oslo, Blindern, Oslo, Norway., Rigling D; Swiss Federal Research Institute WSL, Birmensdorf, Switzerland., Ford KL; School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK., Foster GD; School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK., Pangilinan J; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Papanicolaou A; Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia., Barry K; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., LaButti K; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Virágh M; Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary., Koriabine M; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Yan M; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Riley R; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Champramary S; Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.; Functional Genomics and Bioinformatics Group, Faculty of Forestry, Institute of Forest and Natural Resource Management, University of Sopron, Sopron, Hungary., Plett KL; Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia., Grigoriev IV; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA., Tsai IJ; Biodiversity Research Center, Academia Sinica, Taipei, Taiwan., Slot J; Department of Plant Pathology, The Ohio State University, Columbus, OH, USA., Sipos G; Functional Genomics and Bioinformatics Group, Faculty of Forestry, Institute of Forest and Natural Resource Management, University of Sopron, Sopron, Hungary., Plett J; Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia., Nagy LG; Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary. lnagy@fungenomelab.com.

Publikováno v: Nature microbiology [Nat Microbiol] 2023 Sep; Vol. 8 (9), pp. 1668-1681. Date of Electronic Publication: 2023 Aug 07.

Diversity of genomic adaptations to the post-fire environment in Pezizales fungi points to crosstalk between charcoal tolerance and sexual development.

Autor: Steindorff AS; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Seong K; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA., Carver A; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA., Calhoun S; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Fischer MS; Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA., Stillman K; Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA., Liu H; Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA., Drula E; Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy, 13288 Aix Marseille Université, Marseille, France.; INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques, 13009, Marseille, France., Henrissat B; Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.; DTU Bioengineering, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark., Simpson HJ; Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, MN, 55108, USA., Schilling JS; Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA., Lipzen A; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., He G; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Yan M; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Andreopoulos B; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Pangilinan J; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., LaButti K; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Ng V; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Traxler M; Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA., Bruns TD; Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA., Grigoriev IV; US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA.

Publikováno v: The New phytologist [New Phytol] 2022 Nov; Vol. 236 (3), pp. 1154-1167. Date of Electronic Publication: 2022 Sep 01.

Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2

Autor: Haridas, S., Albert, R., Binder, M., Bloem, J., Labutti, Kurt, Salamov, A., Andreopoulos, B., Baker, S.E., Barry, Kerrie, Bills, G., Bluhm, B.H., Cannon, C., Castanera, R., Culley, D.E., Daum, C., Ezra, D., González, J.B., Henrissat, Bernard, Kuo, A., Liang, C., Lipzen, Anna, Lutzoni, F., Magnuson, J., Mondo, S.J., Nolan, M., Ohm, R.A., Pangilinan, J., Park, H.-J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L.-H., Turgeon, B.G., Goodwin, S.B., Spatafora, J.W., Crous, P.W., Grigoriev, I.V., Ulaganathan, ThirumalaiSelvi, Shi, Rong, Yao, Deqiang, Gu, Ruo-Xu, Garron, Marie-Line, Cherney, Maia, Tieleman, D Peter, Sterner, Eric, Li, Guoyun, Li, Lingyun, Linhardt, Robert, Cygler, Miroslaw, Van Wyk, Niël, Drancourt, Michel, Kremer, Laurent, Miettinen, Otto, Riley, Robert, Cullen, Dan, De Vries, Ronald, Hainaut, Matthieu, Hatakka, Annele, Hildén, Kristiina, Kuo, Rita, Mäkelä, Miia, Sandor, Laura, Spatafora, Joseph, Grigoriev, Igor, Hibbett, David

Publikováno v: Genome Announcements
Genome Announcements, American Society for Microbiology, 2016, 4 (5), pp.112-122. ⟨10.1128/genomeA.00976-16⟩
Genome Announcements, 2016, 4 (5), pp.112-122. ⟨10.1128/genomeA.00976-16⟩
University of Helsinki
Genome announcements, vol 4, iss 5
Genome Announcements, 4(5). American Society for Microbiology

We report here the first genome sequence of the white-rot fungus Obba rivulosa (Polyporales, Basidiomycota), a polypore known for its lignin-decomposing ability. The genome is based on the homokaryon 3A-2 originating in Finland. The genome is typical

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::adcd416ee52ec8c8a09d598e3d8933f2
https://hal-amu.archives-ouvertes.fr/hal-03508713