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1. IMA genome-F18: The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicilliumbiforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1

Author

Visagie, Cobus M., Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A., Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E., Barnes, Irene, Calhoun, Sara, De Angelis, Maria, Frisvad, Jens C., Hakalova, Eliska, Hayes, Richard D., Houbraken, Jos, Grigoriev, Igor V., LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J., Zhang, Yu, and Wingfield, Brenda D.

Published
2023
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8. Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species

Author

Kjærbølling, Inge, Vesth, Tammi C., Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kuo, Alan, Bowyer, Paul, Matsuda, Yudai, Mondo, Stephen, Lyhne, Ellen K., Kogle, Martin E., Clum, Alicia, Lipzen, Anna, Salamov, Asaf, Ngan, Chew Yee, Daum, Chris, Chiniquy, Jennifer, Barry, Kerrie, LaButti, Kurt, Haridas, Sajeet, Simmons, Blake A., Magnuson, Jon K., Mortensen, Uffe H., Larsen, Thomas O., Grigoriev, Igor V., Baker, Scott E., and Andersen, Mikael R.

Published
2018

10. A comparative genomics study of 23 Aspergillus species from section Flavi

Author

Kjærbølling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J. M., Mäkelä, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K., Henrissat, Bernard, Mortensen, Uffe H., Larsen, Thomas O., de Vries, Ronald P., Grigoriev, Igor V., Machida, Masayuki, Baker, Scott E., and Andersen, Mikael R.

Published
2020
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11. Unveiling a classical mutant in the context of the GH3 β-glucosidase family in Neurospora crassa.

Author

Zhang, Yuxin, Nada, Basant, Baker, Scott E., Evans, James E., Tian, Chaoguang, Benz, J. Philipp, and Tamayo, Elisabeth

Subjects
NEUROSPORA crassa, GLUCOSIDASES, CELLULOSE synthase, PLANT cell walls, FILAMENTOUS fungi, DELETION mutation
Abstract

Classical fungal mutant strains obtained by mutagenesis have helped to elucidate fundamental metabolic pathways in the past. In the filamentous fungus Neurospora crassa, the gluc-1 strain was isolated long ago and characterized by its low level of β-glucosidase activity, which is essential for the degradation of cellulose, the most abundant biopolymer on Earth and the main polymeric component of the plant cell wall. Based on genomic resequencing, we hypothesized that the causative mutation resides in the β-glucosidase gene gh3-3 (bgl6, NCU08755). In this work, growth patterns, enzymatic activities and sugar utilization rates were analyzed in several mutant and overexpression strains related to gluc-1 and gh3-3. In addition, different mutants affected in the degradation and transport of cellobiose were analyzed. While overexpression of gh3-3 led to the recovery of β-glucosidase activity in the gluc-1 mutant, as well as normal utilization of cellobiose, the full gene deletion strain Δgh3-3 was found to behave differently than gluc-1 with lower secreted β-glucosidase activity, indicating a dominant role of the amino acid substitution in the point mutated gh3-3 gene of gluc-1. Our results furthermore confirm that GH3-3 is the major extracellular β-glucosidase in N. crassa and demonstrate that the two cellodextrin transporters CDT-1 and CDT-2 are essential for growth on cellobiose when the three main N. crassa β-glucosidases are absent. Overall, these findings provide valuable insight into the mechanisms of cellulose utilization in filamentous fungi, being an essential step in the efficient production of biorefinable sugars from agricultural and forestry plant biomass. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Author

Vesth, Tammi C., Nybo, Jane L., Theobald, Sebastian, Frisvad, Jens C., Larsen, Thomas O., Nielsen, Kristian F., Hoof, Jakob B., Brandl, Julian, Salamov, Asaf, Riley, Robert, Gladden, John M., Phatale, Pallavi, Nielsen, Morten T., Lyhne, Ellen K., Kogle, Martin E., Strasser, Kimchi, McDonnell, Erin, Barry, Kerrie, Clum, Alicia, Chen, Cindy, LaButti, Kurt, Haridas, Sajeet, Nolan, Matt, Sandor, Laura, Kuo, Alan, Lipzen, Anna, Hainaut, Matthieu, Drula, Elodie, Tsang, Adrian, Magnuson, Jon K., Henrissat, Bernard, Wiebenga, Ad, Simmons, Blake A., Mäkelä, Miia R., de Vries, Ronald P., Grigoriev, Igor V., Mortensen, Uffe H., Baker, Scott E., and Andersen, Mikael R.

Published
2018
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19. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Author

Riley, Robert, Salamov, Asaf A., Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitrios, Held, Benjamin W., Levasseur, Anthony, Lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika A., Sun, Hui, LaButti, Kurt M., Schmutz, Jeremy, Jabbour, Dina, Luoi, Hong, Baker, Scott E., Pisabarro, Antonio G., Walton, Jonathan D., Blanchette, Robert A., Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David S., and Grigoriev, Igor V.

Published
2014

26. The Plant Cell Wall—Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

Author

Eastwood, Daniel C., Floudas, Dimitrios, Binder, Manfred, Majcherczyk, Andrzej, Schneider, Patrick, Aerts, Andrea, Asiegbu, Fred O., Baker, Scott E., Barry, Kerrie, Bendiksby, Mika, Blumentritt, Melanie, Coutinho, Pedro M., Cullen, Dan, de Vries, Ronald P., Gathman, Allen, Goodell, Barry, Henrissat, Bernard, Ihrmark, Katarina, Kauserud, Hävard, Kohler, Annegret, LaButti, Kurt, Lapidus, Alla, Lavin, José L., Lee, Yong-Hwan, Lindquist, Erika, Lilly, Walt, Lucas, Susan, Morin, Emmanuelle, Murat, Claude, Oguiza, José A., Park, Jongsun, Pisabarro, Antonio G., Riley, Robert, Rosling, Anna, Salamov, Asaf, Schmidt, Olaf, Schmutz, Jeremy, Skrede, Inger, Stenlid, Jan, Wiebenga, Ad, Xie, Xinfeng, Kües, Ursula, Hibbett, David S., Hoffmeister, Dirk, Högberg, Nils, Martin, Francis, Grigoriev, Igor V., and Watkinson, Sarah C.

Published
2011
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27. Tracking the Roots of Cellulase Hyperproduction by the Fungus Trichoderma Reesei Using Massively Parallel DNA Sequencing

Author

Le Crom, Stéphane, Schackwitz, Wendy, Pennacchio, Len, Magnuson, Jon K., Culley, David E., Collett, James R., Martin, Joel, Druzhinina, Irina S., Mathis, Hugues, Monot, Frédéric, Seiboth, Bernhard, Cherry, Barbara, Rey, Michael, Berka, Randy, Kubicek, Christian P., Baker, Scott E., Margeot, Antoine, and Bennett, Joan Wennstrom

Published
2009
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28. Genome, Transcriptome, and Secretome Analysis of Wood Decay Fungus Postia placenta Supports Unique Mechanisms of Lignocellulose Conversion

Author

Martinez, Diego, Challacombe, Jean, Morgenstern, Ingo, Hibbett, David, Schmoll, Monika, Kubicek, Christian P., Ferreira, Patricia, Ruiz-Duenas, Francisco J., Martinez, Angel T., Kersten, Phil, Hammel, Kenneth E., Vanden Wymelenberg, Amber, Gaskell, Jill, Lindquist, Erika, Sabat, Grzegorz, BonDurant, Sandra Splinter, Larrondo, Luis F., Canessa, Paulo, Vicuna, Rafael, Yadav, Jagjit, Doddapaneni, Harshavardhan, Subramanian, Venkataramanan, Pisabarro, Antonio G., Lavin, José L., Oguiza, José A., Master, Emma, Henrissat, Bernard, Coutinho, Pedro M., Harris, Paul, Magnuson, Jon Karl, Baker, Scott E., Bruno, Kenneth, Kenealy, William, Hoegger, Patrik J., Kües, Ursula, Ramaiya, Preethi, Lucas, Susan, Salamov, Asaf, Shapiro, Harris, Tu, Hank, Chee, Christine L., Misra, Monica, Xie, Gary, Teter, Sarah, Yaver, Debbie, James, Tim, Mokrejs, Martin, Pospisek, Martin, Grigoriev, Igor V., Brettin, Thomas, Rokhsar, Dan, Berka, Randy, Cullen, Dan, and Dixon, Richard A.

Published
2009
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30. The Fusarium graminearum Genome Reveals a Link between Localized Polymorphism and Pathogen Specialization

Author

Cuomo, Christina A., Güldener, Ulrich, Xu, Jin-Rong, Trail, Frances, Turgeon, B. Gillian, Di Pietro, Antonio, Walton, Jonathan D., Ma, Li-Jun, Baker, Scott E., Rep, Martijn, Adam, Gerhard, Antoniw, John, Baldwin, Thomas, Calvo, Sarah, Chang, Yueh-Long, DeCaprio, David, Gale, Liane R., Gnerre, Sante, Goswami, Rubella S., Hammond-Kosack, Kim, Harris, Linda J., Hilburn, Karen, Kennell, John C., Kroken, Scott, Magnuson, Jon K., Mannhaupt, Gertrud, Mauceli, Evan, Mewes, Hans-Werner, Mitterbauer, Rudolf, Muehlbauer, Gary, Münsterkötter, Martin, Nelson, David, O'Donnell, Kerry, Ouellet, Thérèse, Qi, Weihong, Quesneville, Hadi, Roncero, M. Isabel G., Seong, Kye-Yong, Tetko, Igor V., Urban, Martin, Waalwijk, Cees, Ward, Todd J., Yao, Jiqiang, Birren, Bruce W., and Kistler, H. Corby

Published
2007
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33. Identifying the gluc-1 and gluc-2 mutations in Neurospora crassa by genome resequencing.

Author

McCluskey, Kevin and Baker, Scott E.

Abstract

Genome resequencing is an efficient strategy for associating mutant phenotypes with physical genomic loci (Baker 2009). A pilot study of this approach demonstrated that the Neurospora crassa genetic map was critical in narrowing the possible candidate mutations in a strain to a small number in a limited, defined region of the genome (McCluskey et al.2011). In this study, we utilize a resequencing strategy to identify the mutations underlying the gluc-1 and gluc-2 genes in N. crassa. [ABSTRACT FROM AUTHOR]

Published
2022
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37. Fungal genome sequencing and bioenergy

Author

Baker, Scott E., Thykaer, Jette, Adney, William S., Brettin, Thomas S., Brockman, Fred J., D'haeseleer, Patrik, Martinez, A. Diego, Miller, R. Michael, Rokhsar, Daniel S., Schadt, Christopher W., Torok, Tamas, Tuskan, Gerald, Bennett, Joan, Berka, Randy M., Briggs, Steven P., Heitman, Joseph, Taylor, John, Gillian Turgeon, B., Werner-Washburne, Margaret, and Himmel, Michael E.

Published
2008
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41. Genetic interaction between integrins and moleskin, a gene encoding a Drosophila homolog of imporfin-7

Author

Baker, Scott E., Lorenzen, James A., Miller, Steven W., Bunch, Thomas A., Jannuzi, Alison L., Ginsberg, Mark H., Perkins, Lizabeth A., and Brower, Danny L.

Subjects
Genetics -- Research, Gene expression -- Physiological aspects, Epithelial cells -- Genetic aspects, Phenotype -- Genetic aspects, Proteins -- Genetic aspects, Drosophila -- Genetic aspects, Integrins -- Genetic aspects, Biological sciences
Abstract

The Drosophila PS1 and PS2 integrins are required to maintain the connection between the dorsal and ventral wing epithelia. If [alpha]PS subunits are inappropriately expressed during early pupariation, the epithelia separate, causing a wing blister. Two lines of evidence indicate that this apparent loss-of-function phenotype is not a dominant negative effect, but is due to inappropriate expression of functional integrins: wing blisters are not generated efficiently by misexpression of loss-of-function [alpha]PS2 subunits with mutations that inhibit ligand binding, and gain-of-function, hyperactivated mutant [alpha]PS2 proteins cause blistering at expression levels well below those required by wild-type proteins. A genetic screen for dominant suppressors of wing blisters generated null alleles of a gene named moleskin, which encodes the protein DIM-7. DIM-7, a Drosophila homolog of vertebrate importin-7, has recently been shown to bind the SHP-2 tyrosine phosphatase homolog Corkscrew and to be important in the nuclear translocation of activated D-ERK. Consistent with this latter finding, homozygous mutant clones of moleskin fail to grow in the wing. Genetic tests suggest that the moleskin suppression of wing blisters is not directly related to inhibition of D-ERK nuclear import. These data are discussed with respect to the possible regulation of integrin function by cytoplasmic ERK.

Published
2002

43. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Author

Ma, Li-Jun, van der Does, Charlotte H., Borkovich, Katherine A., Coleman, Jeffrey J., Daboussi, Marie-Josée, Di Pietro, Antonio, Dufresne, Marie, Freitag, Michael, Grabherr, Manfred, Henrissat, Bernard, Houterman, Petra M., Kang, Seogchan, Shim, Won-Bo, Woloshuk, Charles, Xie, Xiaohui, Xu, Jin-Rong, Antoniw, John, Baker, Scott E., Bluhm, Burton H., Breakspear, Andrew, Brown, Daren W., Butchko, Robert A. E., Chapman, Sinead, Coulson, Richard, Coutinho, Pedro M., Danchin, Etienne G. J., Diener, Andrew, Gale, Liane R., Gardiner, Donald M., Goff, Stephen, Hammond-Kosack, Kim E., Hilburn, Karen, Hua-Van, Aurélie, Jonkers, Wilfried, Kazan, Kemal, Kodira, Chinnappa D., Koehrsen, Michael, Kumar, Lokesh, Lee, Yong-Hwan, Li, Liande, Manners, John M., Miranda-Saavedra, Diego, Mukherjee, Mala, Park, Gyungsoon, Park, Jongsun, Park, Sook-Young, Proctor, Robert H., Regev, Aviv, Ruiz-Roldan, Carmen M., Sain, Divya, Sakthikumar, Sharadha, Sykes, Sean, Schwartz, David C., Turgeon, Gillian B., Wapinski, Ilan, Yoder, Olen, Young, Sarah, Zeng, Qiandong, Zhou, Shiguo, Galagan, James, Cuomo, Christina A., Kistler, Corby H., and Rep, Martijn

Published
2010
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45. Molecular genetic studies of a human epidermal autoantigen (the 180-kD bullous pemphigoid antigen/BP180): identification of functionally important sequences within the BP180 molecule and evidence for an interaction between BP180 and alpha-6 integrin

Author

Hopkinson, Susan B., Baker, Scott E., and Jones, Jonathan C.R.

Subjects
Autoantigens -- Research, Bullous pemphigoid -- Research, Biological sciences
Abstract

A study of the molecular genetics classifies two functionally important patterns within the noncollagenous domains of the bullous pemphigoid autoantigen (BP180) molecule. BP180, a 180-kD component of the hemidesmosome, is a cell matrix connector and is oriented in a type II fashion in the membrane of the hemidesmosome and is a hybrid collagen. The NH2-terminal sequence is involved in protein polarization while the COOH-terminal noncollagenous domain is required for colocalization with other hemidesmosomal elements such as alpha6 integrin.

Published
1995

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

Author

Kubicek, Christian P, Herrera-Estrella, Alfredo, Seidl-Seiboth, Verena, Martinez, Diego A, Druzhinina, Irina S, Thon, Michael, Zeilinger, Susanne, Casas-Flores, Sergio, Horwitz, Benjamin A, Mukherjee, Prasun K, Mukherjee, Mala, Kredics, László, Alcaraz, Luis D, Aerts, Andrea, Antal, Zsuzsanna, Atanasova, Lea, Cervantes-Badillo, Mayte G, Challacombe, Jean, Chertkov, Olga, McCluskey, Kevin, Coulpier, Fanny, Deshpande, Nandan, von Döhren, Hans, Ebbole, Daniel J, Esquivel-Naranjo, Edgardo U, Fekete, Erzsébet, Flipphi, Michel, Glaser, Fabian, Gómez-Rodríguez, Elida Y, Gruber, Sabine, Han, Cliff, Henrissat, Bernard, Hermosa, Rosa, Hernández-Oñate, Miguel, Karaffa, Levente, Kosti, Idit, Le Crom, Stéphane, Lindquist, Erika, Lucas, Susan, Lübeck, Mette, Lübeck, Peter S, Margeot, Antoine, Metz, Benjamin, Misra, Monica, Nevalainen, Helena, Omann, Markus, Packer, Nicolle, Perrone, Giancarlo, Uresti-Rivera, Edith E, Salamov, Asaf, Schmoll, Monika, Seiboth, Bernhard, Shapiro, Harris, Sukno, Serenella, Tamayo-Ramos, Juan Antonio, Tisch, Doris, Wiest, Aric, Wilkinson, Heather H, Zhang, Michael, Coutinho, Pedro M, Kenerley, Charles M, Monte, Enrique, Baker, Scott E, and Grigoriev, Igor V

Published
2011
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48. A versatile toolkit for high throughput functional genomics with Trichoderma reesei

Author

Schuster André, Bruno Kenneth S, Collett James R, Baker Scott E, Seiboth Bernhard, Kubicek Christian P, and Schmoll Monika

Subjects
Trichoderma reesei, Hypocrea jecorina, transformation, vector construction, gene knock-out library, sexual crossing, Fuel, TP315-360, Biotechnology, TP248.13-248.65
Abstract

Abstract Background The ascomycete fungus, Trichoderma reesei (anamorph of Hypocrea jecorina), represents a biotechnological workhorse and is currently one of the most proficient cellulase producers. While strain improvement was traditionally accomplished by random mutagenesis, a detailed understanding of cellulase regulation can only be gained using recombinant technologies. Results Aiming at high efficiency and high throughput methods, we present here a construction kit for gene knock out in T. reesei. We provide a primer database for gene deletion using the pyr4, amdS and hph selection markers. For high throughput generation of gene knock outs, we constructed vectors using yeast mediated recombination and then transformed a T. reesei strain deficient in non-homologous end joining (NHEJ) by spore electroporation. This NHEJ-defect was subsequently removed by crossing of mutants with a sexually competent strain derived from the parental strain, QM9414. Conclusions Using this strategy and the materials provided, high throughput gene deletion in T. reesei becomes feasible. Moreover, with the application of sexual development, the NHEJ-defect can be removed efficiently and without the need for additional selection markers. The same advantages apply for the construction of multiple mutants by crossing of strains with different gene deletions, which is now possible with considerably less hands-on time and minimal screening effort compared to a transformation approach. Consequently this toolkit can considerably boost research towards efficient exploitation of the resources of T. reesei for cellulase expression and hence second generation biofuel production.

Published
2012
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49. Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey

Author

Herrera-Estrella Alfredo, Grigoriev Igor, Sun Jibin, Schmoll Monika, Martínez Pedro, Zeilinger Susanne, Koptchinskiy Alexeji, Gruber Sabine, Lindquist Erika, Song Lifu, Seidl Verena, Baker Scott E, and Kubicek Christian P

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Combating the action of plant pathogenic microorganisms by mycoparasitic fungi has been announced as an attractive biological alternative to the use of chemical fungicides since two decades. The fungal genus Trichoderma includes a high number of taxa which are able to recognize, combat and finally besiege and kill their prey. Only fragments of the biochemical processes related to this ability have been uncovered so far, however. Results We analyzed genome-wide gene expression changes during the begin of physical contact between Trichoderma atroviride and two plant pathogens Botrytis cinerea and Rhizoctonia solani, and compared with gene expression patterns of mycelial and conidiating cultures, respectively. About 3000 ESTs, representing about 900 genes, were obtained from each of these three growth conditions. 66 genes, represented by 442 ESTs, were specifically and significantly overexpressed during onset of mycoparasitism, and the expression of a subset thereof was verified by expression analysis. The upregulated genes comprised 18 KOG groups, but were most abundant from the groups representing posttranslational processing, and amino acid metabolism, and included components of the stress response, reaction to nitrogen shortage, signal transduction and lipid catabolism. Metabolic network analysis confirmed the upregulation of the genes for amino acid biosynthesis and of those involved in the catabolism of lipids and aminosugars. Conclusion The analysis of the genes overexpressed during the onset of mycoparasitism in T. atroviride has revealed that the fungus reacts to this condition with several previously undetected physiological reactions. These data enable a new and more comprehensive interpretation of the physiology of mycoparasitism, and will aid in the selection of traits for improvement of biocontrol strains by recombinant techniques.

Published
2009
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50. Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

Author

Grigoriev Igor V, Gaskell Simon J, Riba-Garcia Isabel, Francis-McIntyre Sue, Sugden Deana, Wright James C, Baker Scott E, Beynon Robert J, and Hubbard Simon J

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI) and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS) were acquired from 1d gel electrophoresis bands and searched against all available gene models using Average Peptide Scoring (APS) and reverse database searching to produce confident identifications at an acceptable false discovery rate (FDR). Results 405 identified peptide sequences were mapped to 214 different A.niger genomic loci to which 4093 predicted gene models clustered, 2872 of which contained the mapped peptides. Interestingly, 13 (6%) of these loci either had no preferred predicted gene model or the genome annotators' chosen "best" model for that genomic locus was not found to be the most parsimonious match to the identified peptides. The peptides identified also boosted confidence in predicted gene structures spanning 54 introns from different gene models. Conclusion This work highlights the potential of integrating experimental proteomics data into genomic annotation pipelines much as expressed sequence tag (EST) data has been. A comparison of the published genome from another strain of A.niger sequenced by DSM showed that a number of the gene models or proteins with proteomics evidence did not occur in both genomes, further highlighting the utility of the method.

Published
2009
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