Fungal and Algal Pubs

All JGI Publications

2024

Bálint, Balázs et al. (2024) ContScout: sensitive detection and removal of contamination from annotated genomes. Nature Communications 15(1), 936. 10.1038/s41467-024-45024-5
Baroncelli, Riccardo et al. (2024) Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi. GigaScience 13, giae036. 10.1093/gigascience/giae036
Baroncelli, Riccardo et al. (2024) Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi. GigaScience 13, giae036. 10.1093/gigascience/giae036
Barros, Katharina O. et al. (2024) Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces. Biotechnology for Biofuels and Bioproducts 17(1), 20. 10.1186/s13068-024-02467-8
Ben Ayed, Amal et al. (2024) Genome sequencing of Porostereum spadiceum to study the degradation of levofloxacin. Ecotoxicology and Environmental Safety 270, 115808. 10.1016/j.ecoenv.2023.115808
Czajka, Jeffrey J. et al. (2024) Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces. Frontiers in Bioengineering and Biotechnology 12, 1356551. 10.3389/fbioe.2024.1356551
Czajka, Jeffrey J. et al. (2024) Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces. Frontiers in Bioengineering and Biotechnology 12, 1356551. 10.3389/fbioe.2024.1356551
Dziuba, Marcin K. et al. (2024) Phylogeny, morphology, virulence, ecology, and host range of Ordospora pajunii (Ordosporidae), a microsporidian symbiont of Daphnia spp.. mBio 15(6), e00582-24. 10.1128/mbio.00582-24
Dziuba, Marcin K. et al. (2024) Phylogeny, morphology, virulence, ecology, and host range of Ordospora pajunii (Ordosporidae), a microsporidian symbiont of Daphnia spp.. mBio 15(6), e00582-24. 10.1128/mbio.00582-24
Eichfeld, Ruben et al. (2024) Transcriptomics reveal a mechanism of niche defense: two beneficial root endophytes deploy an antimicrobial GH18‐CBM5 chitinase to protect their hosts. New Phytologist . 10.1111/nph.20080
Eichfeld, Ruben et al. (2024) Transcriptomics reveal a mechanism of niche defense: two beneficial root endophytes deploy an antimicrobial GH18‐CBM5 chitinase to protect their hosts. New Phytologist . 10.1111/nph.20080
Felipe Benites, L. et al. (2024) Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts. Communications Biology 7(1), 312. 10.1038/s42003-024-05931-1
Felipe Benites, L. et al. (2024) Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts. Communications Biology 7(1), 312. 10.1038/s42003-024-05931-1
Feng, Xuehuan et al. (2024) Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nature Genetics 56(5), 1018-1031. 10.1038/s41588-024-01737-3
Feng, Xuehuan et al. (2024) Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nature Genetics 56(5), 1018-1031. 10.1038/s41588-024-01737-3
Freyria, Nastasia J. et al. (2024) Stress responses in an Arctic microalga (Pelagophyceae) following sudden salinity change revealed by gene expression analysis. Communications Biology 7(1), 1084. 10.1038/s42003-024-06765-7
Freyria, Nastasia J. et al. (2024) Stress responses in an Arctic microalga (Pelagophyceae) following sudden salinity change revealed by gene expression analysis. Communications Biology 7(1), 1084. 10.1038/s42003-024-06765-7
Gomez-Gutierrrez, Sandra V. et al. (2024) Comparative genomics of the extremophile Cryomyces antarcticus and other psychrophilic Dothideomycetes. Frontiers in Fungal Biology 5, 1418145. 10.3389/ffunb.2024.1418145
Gomez-Gutierrrez, Sandra V. et al. (2024) Comparative genomics of the extremophile Cryomyces antarcticus and other psychrophilic Dothideomycetes. Frontiers in Fungal Biology 5, 1418145. 10.3389/ffunb.2024.1418145
Harder, Christoffer Bugge et al. (2024) Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. Cell Genomics 4(7), 100586. 10.1016/j.xgen.2024.100586
Harder, Christoffer Bugge et al. (2024) Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. Cell Genomics 4(7), 100586. 10.1016/j.xgen.2024.100586
Jiménez, Idoia et al. (2024) In silico analysis of the expression profile of AA9 Lytic Polysaccharide Monooxygenases (LPMOs) and the CDH Cellobiose Dehydrogenase enzyme in wood-degrader Agaricomycetes. The Pleurotus ostreatus case. Current Research in Biotechnology 8, 100244. 10.1016/j.crbiot.2024.100244
Jiménez, Idoia et al. (2024) In silico analysis of the expression profile of AA9 Lytic Polysaccharide Monooxygenases (LPMOs) and the CDH Cellobiose Dehydrogenase enzyme in wood-degrader Agaricomycetes. The Pleurotus ostreatus case. Current Research in Biotechnology 8, 100244. 10.1016/j.crbiot.2024.100244
Kraisitudomsook, Nattapol et al. (2024) On the origin of bird’s nest fungi: Phylogenomic analyses of fungi in the Nidulariaceae (Agaricales, Basidiomycota). Molecular Phylogenetics and Evolution 193, 108010. 10.1016/j.ympev.2024.108010
Lax, Carlos et al. (2024) Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales. Nature Communications 15(1), 6066. 10.1038/s41467-024-50365-2
Lax, Carlos et al. (2024) Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales. Nature Communications 15(1), 6066. 10.1038/s41467-024-50365-2
Liu, Dujuan et al. (2024) AraR plays a more dominant role than XlnR in plant biomass conversion in Penicillium subrubescens. Current Research in Biotechnology 8, 100243. 10.1016/j.crbiot.2024.100243
Liu, Dujuan et al. (2024) AraR plays a more dominant role than XlnR in plant biomass conversion in Penicillium subrubescens. Current Research in Biotechnology 8, 100243. 10.1016/j.crbiot.2024.100243
Lofgren, Lotus et al. (2024) Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. New Phytologist 242(4), 1448-1475. 10.1111/nph.19700
Lofgren, Lotus et al. (2024) Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. New Phytologist 242(4), 1448-1475. 10.1111/nph.19700
Maini Rekdal, Vayu et al. (2024) Neurospora intermedia from a traditional fermented food enables waste-to-food conversion. Nature Microbiology , 1-18. 10.1038/s41564-024-01799-3
Maini Rekdal, Vayu et al. (2024) Neurospora intermedia from a traditional fermented food enables waste-to-food conversion. Nature Microbiology , 1-18. 10.1038/s41564-024-01799-3
Marian, Ioana M et al. (2024) High phenotypic and genotypic plasticity among strains of the mushroom-forming fungus Schizophyllum commune. Fungal Genetics and Biology 173, 103913. 10.1016/j.fgb.2024.103913
Marian, Ioana M et al. (2024) High phenotypic and genotypic plasticity among strains of the mushroom-forming fungus Schizophyllum commune. Fungal Genetics and Biology 173, 103913. 10.1016/j.fgb.2024.103913
Marqués‐Gálvez, José Eduardo et al. (2024) Populus MYC2 orchestrates root transcriptional reprogramming of defence pathway to impair Laccaria bicolor ectomycorrhizal development. New Phytologist 242(2), 658-674. 10.1111/nph.19609
Martin, Francis M. et al. (2024) The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. New Phytologist 242(4), 1486-1506. 10.1111/nph.19541
Martin, Francis M. et al. (2024) The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. New Phytologist 242(4), 1486-1506. 10.1111/nph.19541
Mathieu, Davis et al. (2024) Multilevel analysis between Physcomitrium patens and Mortierellaceae endophytes explores potential long‐standing interaction among land plants and fungi. The Plant Journal 118(2), 304-323. 10.1111/tpj.16605
Navarro, David et al. (2024) Draft genome sequencing and assembly of Favolaschia claudopus CIRM-BRFM 2984 isolated from oak limbs. Journal of Genomics 12, 44-46. 10.7150/jgen.92255
Oliver, Tiffany et al. (2024) Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota. Scientific Data 11(1), 966. 10.1038/s41597-024-03826-8
Oliver, Tiffany et al. (2024) Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota. Scientific Data 11(1), 966. 10.1038/s41597-024-03826-8
Pellitier, Peter T et al. (2024) Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient. ISME Communications 4(1), ycae031. 10.1093/ismeco/ycae031
Ramos, Victor M. Gonzalez et al. (2024) Transcriptional response of the white-rot fungus Dichomitus squalens to polysaccharides reveals a co-expression network of plant biomass conversion related genes. Current Research in Biotechnology 7, 100198. 10.1016/j.crbiot.2024.100198
Roman, Victor A et al. (2024) Identification and recombinant expression of a cutinase from Papiliotrema laurentii that hydrolyzes natural and synthetic polyesters.. Applied and Environmental Microbiology 90(5), e0169423. 10.1128/aem.01694-23
Roman, Victor A et al. (2024) Identification and recombinant expression of a cutinase from Papiliotrema laurentii that hydrolyzes natural and synthetic polyesters.. Applied and Environmental Microbiology 90(5), e0169423. 10.1128/aem.01694-23
Roman, Victor A. et al. (2024) Draft genome sequence of the Tremellomycetes yeast Papiliotrema laurentii 5307AH, isolated from aircraft. Microbiology Resource Announcements 13(8), e00141-24. 10.1128/mra.00141-24
Roman, Victor A. et al. (2024) Draft genome sequence of the Tremellomycetes yeast Papiliotrema laurentii 5307AH, isolated from aircraft. Microbiology Resource Announcements 13(8), e00141-24. 10.1128/mra.00141-24
Rosling, Anna et al. (2024) Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis. BMC Genomics 25(1), 529. 10.1186/s12864-024-10391-2
Rosling, Anna et al. (2024) Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis. BMC Genomics 25(1), 529. 10.1186/s12864-024-10391-2
Smith, Alexander et al. (2024) Comparative transcriptomics provides insights into molecular mechanisms of zinc tolerance in the ectomycorrhizal fungus Suillus luteus. G3: Genes, Genomes, Genetics 14(9), jkae156. 10.1093/g3journal/jkae156
Smith, Alexander et al. (2024) Comparative transcriptomics provides insights into molecular mechanisms of zinc tolerance in the ectomycorrhizal fungus Suillus luteus. G3: Genes, Genomes, Genetics 14(9), jkae156. 10.1093/g3journal/jkae156
Stajich, Jason E et al. (2024) Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. eLife 12, rp92863. 10.7554/elife.92863
Stajich, Jason E et al. (2024) Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. eLife 12, rp92863. 10.7554/elife.92863
Theobald, Sebastian et al. (2024) Genomic Analysis of Aspergillus Section Terrei Reveals a High Potential in Secondary Metabolite Production and Plant Biomass Degradation. Journal of Fungi 10(7), 507. 10.3390/jof10070507
Theobald, Sebastian et al. (2024) Genomic Analysis of Aspergillus Section Terrei Reveals a High Potential in Secondary Metabolite Production and Plant Biomass Degradation. Journal of Fungi 10(7), 507. 10.3390/jof10070507
Van Etten, Julia et al. (2024) Diverse fates of ancient horizontal gene transfers in extremophilic red algae. Environmental Microbiology 26(5), e16629. 10.1111/1462-2920.16629
Van Etten, Julia et al. (2024) Diverse fates of ancient horizontal gene transfers in extremophilic red algae. Environmental Microbiology 26(5), e16629. 10.1111/1462-2920.16629
van Ingen-Buijs, Valerie A et al. (2024) Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses. Fungal Genetics and Biology 175, 103925. 10.1016/j.fgb.2024.103925
van Ingen-Buijs, Valerie A et al. (2024) Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses. Fungal Genetics and Biology 175, 103925. 10.1016/j.fgb.2024.103925
Zhang, Yong et al. (2024) Virulence of banana wilt-causing fungal pathogen Fusarium oxysporum tropical race 4 is mediated by nitric oxide biosynthesis and accessory genes. Nature Microbiology 9(9), 2232-2243. 10.1038/s41564-024-01779-7
Zhang, Yong et al. (2024) Virulence of banana wilt-causing fungal pathogen Fusarium oxysporum tropical race 4 is mediated by nitric oxide biosynthesis and accessory genes. Nature Microbiology 9(9), 2232-2243. 10.1038/s41564-024-01779-7

2023

Akparov, Zeynal et al. (2023) Two major chromosome evolution events with unrivaled conserved gene content in pomegranate. Frontiers in Plant Science 14, 1039211. 10.3389/fpls.2023.1039211
Amses, Kevin et al. (2023) Convergent reductive evolution and host adaptation in Mycoavidus bacterial endosymbionts of Mortierellaceae fungi. Fungal Genetics and Biology 169, 103838. 10.1016/j.fgb.2023.103838
Auer, Lucas et al. (2023) Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems. New Phytologist . 10.1111/nph.19471
Barrett, Kristian et al. (2023) Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes.. Nucleic Acids Research 51(W1), w108-w114. 10.1093/nar/gkad385
Brown, Jennifer L. et al. (2023) High-quality RNA extraction and the regulation of genes encoding cellulosomes are correlated with growth stage in anaerobic fungi. Frontiers in Fungal Biology 4, 1171100. 10.3389/ffunb.2023.1171100
Carr, Erin C et al. (2023) Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche.. G3: Genes, Genomes, Genetics . 10.1093/g3journal/jkad110
Crandall, Johnathan G. et al. (2023) Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism. PLOS Biology 21(11), e3001909. 10.1371/journal.pbio.3001909
Crandall, Johnathan G. et al. (2023) Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism. PLOS Biology 21(11), e3001909. 10.1371/journal.pbio.3001909
Crandall, Johnathan G. et al. (2023) Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism. PLOS Biology 21(11), e3001909. 10.1371/journal.pbio.3001909
de Oliveira, Camilla Martins et al. (2023) Trichoderma harzianum transcriptome in response to the nematode Pratylenchus brachyurus. Biological Control 183, 105245. 10.1016/j.biocontrol.2023.105245
Diesel, Jose et al. (2023) A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera). BMC Genomics 24(1), 543. 10.1186/s12864-023-09658-x
Dort, E. N. et al. (2023) Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits. Scientific Reports 13(1), 17203. 10.1038/s41598-023-44005-w
Dort, E. N. et al. (2023) Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits. Scientific Reports 13(1), 17203. 10.1038/s41598-023-44005-w
Dort, E. N. et al. (2023) Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits. Scientific Reports 13(1), 17203. 10.1038/s41598-023-44005-w
Duncan, Anthony et al. (2023) Dataset of 143 metagenome-assembled genomes from the Arctic and Atlantic Oceans, including 21 for eukaryotic organisms. Data in Brief 47, 108990. 10.1016/j.dib.2023.108990
Feurtey, Alice et al. (2023) A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen. Nature Communications 14(1), 1059. 10.1038/s41467-023-36674-y
Gryganskyi, Andrii P. et al. (2023) Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?. Microorganisms 11(7), 1830. 10.3390/microorganisms11071830
Guerillot, Pamela et al. (2023) A Remarkable Expansion of Oligopeptide Transporter Genes in Rust Fungi (Pucciniales) Suggests a Specialization in Nutrient Acquisition for Obligate Biotrophy.. Phytopathology 113(2), 252-264. 10.1094/phyto-04-22-0128-r
Gupta, Yogesh K. et al. (2023) Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi. Nature Communications 14(1), 1835. 10.1038/s41467-023-37551-4
Hage, Hayat et al. (2023) An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi. Microbial Genomics 9(4), mgen000990. 10.1099/mgen.0.000990
Haridas, Sajeet et al. (2023) T-Toxin Virulence Genes: Unconnected Dots in a Sea of Repeats. mBio 14(2), e00261-23. 10.1128/mbio.00261-23
Hensen, Noah et al. (2023) Genome-scale phylogeny and comparative genomics of the fungal order Sordariales. Molecular Phylogenetics and Evolution 189, 107938. 10.1016/j.ympev.2023.107938
Hensen, Noah et al. (2023) Genome-scale phylogeny and comparative genomics of the fungal order Sordariales. Molecular Phylogenetics and Evolution 189, 107938. 10.1016/j.ympev.2023.107938
Hensen, Noah et al. (2023) Genome-scale phylogeny and comparative genomics of the fungal order Sordariales. Molecular Phylogenetics and Evolution 189, 107938. 10.1016/j.ympev.2023.107938
Hooker, Casey A. et al. (2023) A Genetic Engineering Toolbox for the Lignocellulolytic Anaerobic Gut Fungus Neocallimastix frontalis. ACS Synthetic Biology 12(4), 1034-1045. 10.1021/acssynbio.2c00502
Jagtap, Sujit Sadashiv et al. (2023) Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates. Microbiology Resource Announcements 12(12), e00435-23. 10.1128/mra.00435-23
Jagtap, Sujit Sadashiv et al. (2023) Near-complete genome sequence of Lipomyces tetrasporous NRRL Y-64009, an oleaginous yeast capable of growing on lignocellulosic hydrolysates. Microbiology Resource Announcements 12(11), e00426-23. 10.1128/mra.00426-23
Jagtap, Sujit Sadashiv et al. (2023) Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates. Microbiology Resource Announcements 12(12), e00435-23. 10.1128/mra.00435-23
Jagtap, Sujit Sadashiv et al. (2023) Near-complete genome sequence of Lipomyces tetrasporous NRRL Y-64009, an oleaginous yeast capable of growing on lignocellulosic hydrolysates. Microbiology Resource Announcements 12(11), e00426-23. 10.1128/mra.00426-23
Jagtap, Sujit Sadashiv et al. (2023) Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates. Microbiology Resource Announcements 12(12), e00435-23. 10.1128/mra.00435-23
Jagtap, Sujit Sadashiv et al. (2023) Near-complete genome sequence of Lipomyces tetrasporous NRRL Y-64009, an oleaginous yeast capable of growing on lignocellulosic hydrolysates. Microbiology Resource Announcements 12(11), e00426-23. 10.1128/mra.00426-23
Ke, Yi-Hong et al. (2023) Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi.. Genetics 224(2). 10.1093/genetics/iyad069
Kun, Roland S et al. (2023) The transcriptional activator ClrB is crucial for the degradation of soybean hulls and guar gum in Aspergillus niger. Fungal Genetics and Biology 165, 103781. 10.1016/j.fgb.2023.103781
Kun, Roland S et al. (2023) The Amylolytic Regulator AmyR of Aspergillus niger Is Involved in Sucrose and Inulin Utilization in a Culture-Condition-Dependent Manner. Journal of Fungi 9(4), 438. 10.3390/jof9040438
Lankiewicz, Thomas S. et al. (2023) Lignin deconstruction by anaerobic fungi. Nature Microbiology 8(4), 596-610. 10.1038/s41564-023-01336-8
Leng, Yueqiang et al. (2023) A telomere-to-telomere genome assembly resource of Bipolaris sorokiniana, the fungal pathogen causing spot blotch and common root rot diseases in barley and wheat. PhytoFrontiers™ . 10.1094/phytofr-08-23-0108-a
Li, Jiajia et al. (2023) Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi. Journal of Fungi 9(8), 860. 10.3390/jof9080860
Li, Ye et al. (2023) Plasmid Copy Number Engineering Accelerates Fungal Polyketide Discovery upon Unnatural Polyketide Biosynthesis. ACS Synthetic Biology 12(8), 2226-2235. 10.1021/acssynbio.3c00178
Longley, Reid et al. (2023) Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi. Communications Biology 6(1), 948. 10.1038/s42003-023-05299-8
Maillard, François et al. (2023) Functional genomics gives new insights into the ectomycorrhizal degradation of chitin. New Phytologist 238(2), 845-858. 10.1111/nph.18773
McRae, Amanda G. et al. (2023) Spray‐induced gene silencing to identify powdery mildew gene targets and processes for powdery mildew control. Molecular Plant Pathology . 10.1111/mpp.13361
Min, Byoungnam et al. (2023) Transcriptomics of Temporal- versus Substrate-Specific Wood Decay in the Brown-Rot Fungus Fibroporia radiculosa. Journal of Fungi 9(10), 1029. 10.3390/jof9101029
Min, Byoungnam et al. (2023) Transcriptomics of Temporal- versus Substrate-Specific Wood Decay in the Brown-Rot Fungus Fibroporia radiculosa. Journal of Fungi 9(10), 1029. 10.3390/jof9101029
Min, Byoungnam et al. (2023) Transcriptomics of Temporal- versus Substrate-Specific Wood Decay in the Brown-Rot Fungus Fibroporia radiculosa. Journal of Fungi 9(10), 1029. 10.3390/jof9101029
Plett, Jonathan M et al. (2023) Speciation Underpinned by Unexpected Molecular Diversity in the Mycorrhizal Fungal Genus Pisolithus. Molecular Biology and Evolution 40(3), msad045. 10.1093/molbev/msad045
Reynolds, Nicole K et al. (2023) Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi. Genome Biology and Evolution 15(1), evac185. 10.1093/gbe/evac185
Riley, Robert et al. (2023) Terabase-Scale Coassembly of a Tropical Soil Microbiome. Microbiology Spectrum , e00200-23. 10.1128/spectrum.00200-23
Sahu, Neha et al. (2023) Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria. Nature Microbiology 8(9), 1668-1681. 10.1038/s41564-023-01448-1
Santos-Pascual, Rodrigo et al. (2023) Deciphering the molecular components of the quorum sensing system in the fungus Ophiostoma piceae. Microbiology Spectrum 11(6), e00290-23. 10.1128/spectrum.00290-23
Santos-Pascual, Rodrigo et al. (2023) Deciphering the molecular components of the quorum sensing system in the fungus Ophiostoma piceae. Microbiology Spectrum 11(6), e00290-23. 10.1128/spectrum.00290-23
Santos-Pascual, Rodrigo et al. (2023) Deciphering the molecular components of the quorum sensing system in the fungus Ophiostoma piceae. Microbiology Spectrum 11(6), e00290-23. 10.1128/spectrum.00290-23
Sierra-Patev, Sean et al. (2023) A global phylogenomic analysis of the shiitake genus Lentinula. Proceedings of the National Academy of Sciences of the United States of America 120(10), e2214076120. 10.1073/pnas.2214076120
Steele, Taylor S. et al. (2023) Biosynthesis of Haloterpenoids in Red Algae via Microbial-like Type I Terpene Synthases. ACS Chemical Biology 19(1), 185-192. 10.1021/acschembio.3c00627
Steele, Taylor S. et al. (2023) Biosynthesis of Haloterpenoids in Red Algae via Microbial-like Type I Terpene Synthases. ACS Chemical Biology 19(1), 185-192. 10.1021/acschembio.3c00627
Steele, Taylor S. et al. (2023) Biosynthesis of Haloterpenoids in Red Algae via Microbial-like Type I Terpene Synthases. ACS Chemical Biology 19(1), 185-192. 10.1021/acschembio.3c00627
Stuart, Emiko K et al. (2023) Acquisition of host-derived carbon in biomass of the ectomycorrhizal fungus Pisolithus microcarpus is correlated to fungal carbon demand and plant defences. FEMS Microbiology Ecology 99(5), fiad037. 10.1093/femsec/fiad037
Vigneaud, Julien et al. (2023) DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus. New Phytologist 238(6), 2561-2577. 10.1111/nph.18734
Visagie, Cobus M. et al. (2023) IMA genome-F18. IMA Fungus 14(1), 21. 10.1186/s43008-023-00121-w
Visagie, Cobus M. et al. (2023) IMA genome-F18. IMA Fungus 14(1), 21. 10.1186/s43008-023-00121-w
Visagie, Cobus M. et al. (2023) IMA genome-F18. IMA Fungus 14(1), 21. 10.1186/s43008-023-00121-w
Vittorelli, Nina et al. (2023) Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores. PLOS Genetics 19(2), e1010347. 10.1371/journal.pgen.1010347
Wang, Yan et al. (2023) Divergent Evolution of Early Terrestrial Fungi Reveals the Evolution of Mucormycosis Pathogenicity Factors. Genome Biology and Evolution 15(4), evad046. 10.1093/gbe/evad046
Winder, Johanna C. et al. (2023) Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean. Genes 14(2), 363. 10.3390/genes14020363
Wyczanska, Maja et al. (2023) Local-scale panmixia in the lichenized fungus Xanthoria parietina contrasts with substantial genetic structure in its Trebouxia photobionts. The Lichenologist 55(2), 69-79. 10.1017/s002428292300004x
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2022

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2021

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2020

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Wu, V. W. et al. (2020) The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus. Proc Natl Acad Sci U S A 117(11), 6003-6013. 10.1073/pnas.1915611117

2019

Almasi, E. et al. (2019) Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae. New Phytol . 10.1111/nph.16032
Almasi, E. et al. (2019) Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae. New Phytol . 10.1111/nph.16032
Alvarez-Escribano, I. et al. (2019) Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants. BMC Biol 17(1), 88. 10.1186/s12915-019-0702-0
Anasontzis, G. E. et al. (2019) Broad-specificity GH131 beta-glucanases are a hallmark of Fungi and Oomycetes that colonise plants. Environ Microbiol . 10.1111/1462-2920.14596
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Benocci, T. et al. (2019) Enzymatic Adaptation of Podospora anserina to Different Plant Biomass Provides Leads to Optimized Commercial Enzyme Cocktails. Biotechnol J 14(4), e1800185. 10.1002/biot.201800185
Benucci, G. M. N. et al. (2019) Draft Genome Sequence of the Ectomycorrhizal Ascomycete Sphaerosporella brunnea. Microbiol Resour Announc 8(50). 10.1128/MRA.00857-19
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Plett, K. L. et al. (2019) Inorganic nitrogen availability alters Eucalyptus grandis receptivity to the ectomycorrhizal fungus Pisolithus albus but not symbiotic nitrogen transfer. New Phytol . 10.1111/nph.16322
Robinson, A. J. et al. (2019) Diverse members of the Xylariales lack canonical mating-type regions. Fungal Genet Biol 122, 47-52. 10.1016/j.fgb.2018.12.004
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Wu, B. et al. (2019) Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi. ISME J . 10.1038/s41396-019-0359-2

2018

Aguilar-Pontes, M. V. et al. (2018) The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi. Studies in mycology 91, 61-78. 10.1016/j.simyco.2018.10.001
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Daly, P. et al. (2018) Dichomitus squalens partially tailors its molecular responses to the composition of solid wood. Environ Microbiol . 10.1111/1462-2920.14416
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Emri, T. et al. (2018) Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance. Studies in mycology 91, 23-36. 10.1016/j.simyco.2018.10.003
Grum-Grzhimaylo, A. A. et al. (2018) The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet. Mol Ecol . 10.1111/mec.14912
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Varriale, S. et al. (2018) Talaromyces borbonicus, sp. nov., a novel fungus from biodegraded Arundo donax with potential abilities in lignocellulose conversion. Mycologia 110(2), 316-324. 10.1080/00275514.2018.1456835
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Wu, B. et al. (2018) Substrate-Specific Differential Gene Expression and RNA editing in the Brown Rot Fungus Fomitopsis pinicola. Appl Environ Microbiol 84(16). 10.1128/AEM.00991-18
Wu, B. et al. (2018) Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies. Genome Biol Evol 10(12), 3250-3261. 10.1093/gbe/evy246

2017

Aime, M. C. et al. (2017) Phylogenetics and Phylogenomics of Rust Fungi. Adv Genet 100, 267-307. 10.1016/bs.adgen.2017.09.011
Blanc-Mathieu, R. et al. (2017) Population genomics of picophytoplankton unveils novel chromosome hypervariability. Sci Adv 3(7), e1700239. 10.1126/sciadv.1700239
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de Vries, R. P. et al. (2017) Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 18(1), 28. 10.1186/s13059-017-1151-0
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Fochi, V. et al. (2017) Fungal and plant gene expression in the Tulasnella calospora-Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas. New Phytol 213(1), 365-379. 10.1111/nph.14279
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Magain, N. et al. (2017) Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen -forming genus Peltigera section Polydactylon. Molecular Phylogenetics and Evolution 117, 10-29. 10.1016/j.ympev.2017.08.013
Min, B. et al. (2017) FunGAP: Fungal Genome Annotation Pipeline Using Evidence-based Gene Model Evaluation. Bioinformatics . 10.1093/bioinformatics/btx353
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Mujic, A. B. et al. (2017) Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus. G3 (Bethesda) 7(6), 1775-1789. 10.1534/g3.117.039396
Mujic, A. B. et al. (2017) Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus. G3 (Bethesda) 7(6), 1775-1789. 10.1534/g3.117.039396
Nagy, L. G. et al. (2017) Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution. Mol Biol Evol 34(1), 35-44. 10.1093/molbev/msw238
Peng, M. et al. (2017) The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi. J Biotechnol 246, 1-3. 10.1016/j.jbiotec.2017.02.012
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Robicheau, B. M. et al. (2017) The complete mitochondrial genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 confirms evolutionary division within the fungal Phialocephala fortinii s.l. – Acephala appalanata species complex. Fungal Biol 121(3), 212-221. 10.1016/j.funbio.2016.11.007
Robicheau, B. M. et al. (2017) The homothallic mating-type locus of the conifer needle endophyte Phialocephala scopiformis DAOMC 229536 (order Helotiales). Fungal Biol 121(12), 1011-1024. 10.1016/j.funbio.2017.08.007
Robicheau, B. M. et al. (2017) The homothallic mating-type locus of the conifer needle endophyte Phialocephala scopiformis DAOMC 229536 (order Helotiales). Fungal Biol 121(12), 1011-1024. 10.1016/j.funbio.2017.08.007
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Thieme, N. et al. (2017) The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa. Biotechnol Biofuels 10, 149. 10.1186/s13068-017-0807-z
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Xiong, Y. et al. (2017) A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism. PLoS Genet 13(5), e1006737. 10.1371/journal.pgen.1006737

2016

Alfaro, M. et al. (2016) Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungus Pleurotus ostreatus. Environ Microbiol . 10.1111/1462-2920.13360
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2015

Baker, S. E. et al. (2015) Draft Genome Sequence of Neurospora crassa Strain FGSC 73. Genome Announc 3(2). 10.1128/genomeA.00074-15
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2014

Chaib De Mares, M. et al. (2014) Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita. New Phytol . 10.1111/nph.13140
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2013

Barriuso, J. et al. (2013) Fungal genomes mining to discover novel sterol esterases and lipases as catalysts. BMC Genomics 14, 712. 10.1186/1471-2164-14-712
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2012

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2011

Andersen, M. R. et al. (2011) Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res 21(6), 885-97. 10.1101/gr.112169.110
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2010

Blanc, G. et al. (2010) The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. Plant Cell 22(9), 2943-55. 10.1105/tpc.110.076406
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2009

Coleman, J. J. et al. (2009) The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion. Plos Genetics 5(8). ARTN e1000618 DOI 10.1371/journal.pgen.1000618
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2008

Bluhm, B. H. et al. (2008) Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth. BMC Genomics 9, 523. 10.1186/1471-2164-9-523
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2007

Jeffries, T. W. et al. (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotechnol 25(3), 319-26. 10.1038/nbt1290
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2006

Baker, S. E. et al. (2006) Aspergillus niger genomics: Past, present and into the future. Medical Mycology 44, S17-S21. Doi 10.1080/13693780600921037
Makarova, K. et al. (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 103(42), 15611-6. 10.1073/pnas.0607117103
Tuskan, G. A. et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793), 1596-1604. Doi 10.1126/Science.1128691
Tyler, B. M. et al. (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313(5791), 1261-1266. Doi 10.1126/Science.1128796
Vanden Wymelenberg, A. et al. (2006) 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. Fungal Genetics and Biology 43(5), 343-356. Doi 10.1016/J.Fgb.2006.01.003

2004

Martin, J. et al. (2004) The sequence and analysis of duplication-rich human chromosome 16. Nature 432(7020), 988-94. 10.1038/nature03187
Martinez, D. et al. (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnology 22(6), 695-700. 10.1038/nbt967
Schmutz, J. et al. (2004) The DNA sequence and comparative analysis of human chromosome 5. Nature 431(7006), 268-74. 10.1038/nature02919