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9. IMA genome-F18

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

Subjects
Microbiology, Plant Biology, Biological Sciences, Plant biology
Published
2023

11. 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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12. Molecular Taxonomy

Author

Hagen, Ferry, Walther, Grit, Houbraken, Jos, Scott, James, Summerbell, Richard, Boekhout, Teun, Hospenthal, Duane R., editor, Rinaldi, Michael G., editor, and Walsh, Thomas J., editor

Published
2023
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18. Talaromyces borbonicus, sp. nov., a novel fungus from biodegraded Arundo donax with potential abilities in lignocellulose conversion

Author

Varriale, Simona, Houbraken, Jos, Granchi, Zoraide, Pepe, Olimpia, Cerullo, Gabriella, Ventorino, Valeria, Chin-A-Woeng, Thomas, Meijer, Martin, Riley, Robert, Grigoriev, Igor V, Henrissat, Bernard, de Vries, Ronald P, and Faraco, Vincenza

Subjects
Microbiology, Biological Sciences, Genetics, Biotechnology, Biotransformation, Carbohydrate Metabolism, Enzymes, Genome, Fungal, Italy, Lignin, Phylogeny, Poaceae, Sequence Analysis, DNA, Talaromyces, Fungi, genome sequence, taxonomy, new taxon, Evolutionary Biology, Plant Biology, Mycology & Parasitology, Evolutionary biology, Plant biology
Abstract

A novel fungal species able to synthesize enzymes with potential synergistic actions in lignocellulose conversion was isolated from the biomass of Arundo donax during biodegradation under natural conditions in the Gussone Park of the Royal Palace of Portici (Naples, Italy). In this work, this species was subjected to morphological and phylogenetic analyses. Sequencing of its genome was performed, resulting in 28 scaffolds that were assembled into 27.05 Mb containing 9744 predicted genes, among which 396 belong to carbohydrate-active enzyme (CAZyme)-encoding genes. Here we describe and illustrate this previously unknown species, which was named Talaromyces borbonicus, by a polyphasic approach combining phenotypic, physiological, and sequence data.

Published
2018

19. Inconsistencies within the proposed framework for stabilizing fungal nomenclature risk further confusion

Author

Kidd, Sarah E., primary, Hagen, Ferry, additional, Halliday, Catriona L., additional, Abdolrasouli, Alireza, additional, Boekhout, Teun, additional, Crous, Pedro W., additional, Ellis, David H., additional, Elvy, Juliet, additional, Forrest, Graeme N., additional, Groenewald, Marizeth, additional, Hahn, Rosane C., additional, Houbraken, Jos, additional, Rodrigues, Anderson M., additional, Scott, James, additional, Sorrell, Tania C., additional, Summerbell, Richard C., additional, Tsui, Clement K. M., additional, Yurkov, Andrey, additional, and Chen, Sharon C.-A., additional

Published
2024
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20. Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

Author

Steenwyk, Jacob L., primary, Balamurugan, Charu, additional, Raja, Huzefa A., additional, Gonçalves, Carla, additional, Li, Ningxiao, additional, Martin, Frank, additional, Berman, Judith, additional, Oberlies, Nicholas H., additional, Gibbons, John G., additional, Goldman, Gustavo H., additional, Geiser, David M., additional, Houbraken, Jos, additional, Hibbett, David S., additional, and Rokas, Antonis, additional

Published
2024
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25. Inconsistencies within the proposed framework for stabilizing fungal nomenclature risk further confusion

Author

Kidd, Sarah E., Hagen, Ferry, Halliday, Catriona L., Abdolrasouli, Alireza, Boekhout, Teun, Crous, Pedro W., Ellis, David H., Elvy, Juliet, Forrest, Graeme N., Groenewald, Marizeth, Hahn, Rosane C., Houbraken, Jos, Rodrigues, Anderson M., Scott, James, Sorrell, Tania C., Summerbell, Richard C., Tsui, Clement K.M., Yurkov, Andrey, Chen, Sharon C.A., Kidd, Sarah E., Hagen, Ferry, Halliday, Catriona L., Abdolrasouli, Alireza, Boekhout, Teun, Crous, Pedro W., Ellis, David H., Elvy, Juliet, Forrest, Graeme N., Groenewald, Marizeth, Hahn, Rosane C., Houbraken, Jos, Rodrigues, Anderson M., Scott, James, Sorrell, Tania C., Summerbell, Richard C., Tsui, Clement K.M., Yurkov, Andrey, and Chen, Sharon C.A.

Published
2024

27. Inconsistencies within the proposed framework for stabilizing fungal nomenclature risk further confusion

Author

MMB, MMB Medische Staf, Kidd, Sarah E., Hagen, Ferry, Halliday, Catriona L., Abdolrasouli, Alireza, Boekhout, Teun, Crous, Pedro W., Ellis, David H., Elvy, Juliet, Forrest, Graeme N., Groenewald, Marizeth, Hahn, Rosane C., Houbraken, Jos, Rodrigues, Anderson M., Scott, James, Sorrell, Tania C., Summerbell, Richard C., Tsui, Clement K.M., Yurkov, Andrey, Chen, Sharon C.A., MMB, MMB Medische Staf, Kidd, Sarah E., Hagen, Ferry, Halliday, Catriona L., Abdolrasouli, Alireza, Boekhout, Teun, Crous, Pedro W., Ellis, David H., Elvy, Juliet, Forrest, Graeme N., Groenewald, Marizeth, Hahn, Rosane C., Houbraken, Jos, Rodrigues, Anderson M., Scott, James, Sorrell, Tania C., Summerbell, Richard C., Tsui, Clement K.M., Yurkov, Andrey, and Chen, Sharon C.A.

Published
2024

28. Aspergillus hubkae, a Novel Species Isolated from a Patient with Probable Invasive Pulmonary Aspergillosis

Author

MMB, MMB Medische Staf, Zhou, Ya Bin, Rezaei-Matehkolaei, Ali, Meijer, Martin, Kraak, Bart, Gerrits van den Ende, Bert, Hagen, Ferry, Afzalzadeh, Sara, Kiasat, Neda, Takesh, Ameneh, Hoseinnejad, Akbar, Houbraken, Jos, MMB, MMB Medische Staf, Zhou, Ya Bin, Rezaei-Matehkolaei, Ali, Meijer, Martin, Kraak, Bart, Gerrits van den Ende, Bert, Hagen, Ferry, Afzalzadeh, Sara, Kiasat, Neda, Takesh, Ameneh, Hoseinnejad, Akbar, and Houbraken, Jos

Published
2024

29. Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

Author

Steenwyk, Jacob L., Balamurugan, Charu, Raja, Huzefa A., Gonçalves, Carla, Li, Ningxiao, Martin, Frank, Berman, Judith, Oberlies, Nicholas H., Gibbons, John G., Goldman, Gustavo H., Geiser, David M., Houbraken, Jos, Hibbett, David S., Rokas, Antonis, Steenwyk, Jacob L., Balamurugan, Charu, Raja, Huzefa A., Gonçalves, Carla, Li, Ningxiao, Martin, Frank, Berman, Judith, Oberlies, Nicholas H., Gibbons, John G., Goldman, Gustavo H., Geiser, David M., Houbraken, Jos, Hibbett, David S., and Rokas, Antonis

Abstract

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.

Published
2024

30. Inconsistencies within the proposed framework for stabilizing fungal nomenclature risk further confusion

Author

Kidd, Sarah E, Hagen, Ferry, Halliday, Catriona L, Abdolrasouli, Alireza, Boekhout, Teun, Crous, Pedro W, Ellis, David H, Elvy, Juliet, Forrest, Graeme N, Groenewald, Marizeth, Hahn, Rosane C, Houbraken, Jos, Rodrigues, Anderson M, Scott, James, Sorrell, Tania C, Summerbell, Richard C, Tsui, Clement K M, Yurkov, Andrey, Chen, Sharon C-A, Kidd, Sarah E, Hagen, Ferry, Halliday, Catriona L, Abdolrasouli, Alireza, Boekhout, Teun, Crous, Pedro W, Ellis, David H, Elvy, Juliet, Forrest, Graeme N, Groenewald, Marizeth, Hahn, Rosane C, Houbraken, Jos, Rodrigues, Anderson M, Scott, James, Sorrell, Tania C, Summerbell, Richard C, Tsui, Clement K M, Yurkov, Andrey, and Chen, Sharon C-A

Published
2024

31. Inconsistencies within the proposed framework for stabilizing fungal nomenclature risk further confusion

Author

Sub Molecular Microbiology, Molecular Microbiology, Kidd, Sarah E., Hagen, Ferry, Halliday, Catriona L., Abdolrasouli, Alireza, Boekhout, Teun, Crous, Pedro W., Ellis, David H., Elvy, Juliet, Forrest, Graeme N., Groenewald, Marizeth, Hahn, Rosane C., Houbraken, Jos, Rodrigues, Anderson M., Scott, James, Sorrell, Tania C., Summerbell, Richard C., Tsui, Clement K.M., Yurkov, Andrey, Chen, Sharon C.A., Sub Molecular Microbiology, Molecular Microbiology, Kidd, Sarah E., Hagen, Ferry, Halliday, Catriona L., Abdolrasouli, Alireza, Boekhout, Teun, Crous, Pedro W., Ellis, David H., Elvy, Juliet, Forrest, Graeme N., Groenewald, Marizeth, Hahn, Rosane C., Houbraken, Jos, Rodrigues, Anderson M., Scott, James, Sorrell, Tania C., Summerbell, Richard C., Tsui, Clement K.M., Yurkov, Andrey, and Chen, Sharon C.A.

Published
2024

40. Domestication in dry‐cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision

Author

Lo, Ying‐Chu, primary, Bruxaux, Jade, additional, Rodríguez de la Vega, Ricardo C., additional, O'Donnell, Samuel, additional, Snirc, Alodie, additional, Coton, Monika, additional, Le Piver, Mélanie, additional, Le Prieur, Stéphanie, additional, Roueyre, Daniel, additional, Dupont, Joëlle, additional, Houbraken, Jos, additional, Debuchy, Robert, additional, Ropars, Jeanne, additional, Giraud, Tatiana, additional, and Branca, Antoine, additional

Published
2023
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42. Fungal diversity notes 1036–1150: taxonomic and phylogenetic contributions on genera and species of fungal taxa

Author

Hyde, Kevin D., Tennakoon, Danushka S., Jeewon, Rajesh, Bhat, D. Jayarama, Maharachchikumbura, Sajeewa S. N., Rossi, Walter, Leonardi, Marco, Lee, Hyang Burm, Mun, Hye Yeon, Houbraken, Jos, Nguyen, Thuong T. T., Jeon, Sun Jeong, Frisvad, Jens Christian, Wanasinghe, Dhanushka N., Lücking, Robert, Aptroot, André, Cáceres, Marcela E. S., Karunarathna, Samantha C., Hongsanan, Sinang, Phookamsak, Rungtiwa, de Silva, Nimali I., Thambugala, Kasun M., Jayawardena, Ruvishika S., Senanayake, Indunil C., Boonmee, Saranyaphat, Chen, Jie, Luo, Zong-Long, Phukhamsakda, Chayanard, Pereira, Olinto L., Abreu, Vanessa P., Rosado, André Wilson Campos, Bart, Buyck, Randrianjohany, Emile, Hofstetter, Valérie, Gibertoni, Tatiana B., Soares, Adriene Mayra da Silva, Plautz, Jr., Helio Longoni, Sotão, Helen Maria Pontes, Xavier, William Kalhy Silva, Bezerra, Jadson Diogo Pereira, de Oliveira, Thays Gabrielle Lins, de Souza-Motta, Cristina Maria, Magalhães, Oliane Maria Correia, Bundhun, Digvijayini, Harishchandra, Dulanjalee, Manawasinghe, Ishara S., Dong, Wei, Zhang, Sheng-Nan, Bao, Dan-Feng, Samarakoon, Milan C., Pem, Dhandevi, Karunarathna, Anuruddha, Lin, Chuan-Gen, Yang, Jing, Perera, Rekhani H., Kumar, Vinit, Huang, Shi-Ke, Dayarathne, Monika C., Ekanayaka, Anusha H., Jayasiri, Subashini C., Xiao, Yuanpin, Konta, Sirinapa, Niskanen, Tuula, Liimatainen, Kare, Dai, Yu-Cheng, Ji, Xiao-Hong, Tian, Xue-Mei, Mešić, Armin, Singh, Sanjay K., Phutthacharoen, Kunthida, Cai, Lei, Sorvongxay, Touny, Thiyagaraja, Vinodhini, Norphanphoun, Chada, Chaiwan, Napalai, Lu, Yong-Zhong, Jiang, Hong-Bo, Zhang, Jin-Feng, Abeywickrama, Pranami D., Aluthmuhandiram, Janith V. S., Brahmanage, Rashika S., Zeng, Ming, Chethana, Thilini, Wei, Deping, Réblová, Martina, Fournier, Jacques, Nekvindová, Jana, do Nascimento Barbosa, Renan, dos Santos, José Ewerton Felinto, de Oliveira, Neiva Tinti, Li, Guo-Jie, Ertz, Damien, Shang, Qiu-Ju, Phillips, Alan J. L., Kuo, Chang-Hsin, Camporesi, Erio, Bulgakov, Timur S., Lumyong, Saisamorn, Jones, E. B. Gareth, Chomnunti, Putarak, Gentekaki, Eleni, Bungartz, Frank, Zeng, Xiang-Yu, Fryar, Sally, Tkalčec, Zdenko, Liang, Junmin, Li, Guangshuo, Wen, Ting-Chi, Singh, Paras Nath, Gafforov, Yusufjon, Promputtha, Itthayakorn, Yasanthika, Erandi, Goonasekara, Ishani D., Zhao, Rui-Lin, Zhao, Qi, Kirk, Paul M., Liu, Jian-Kui, Yan, JiYe, Mortimer, Peter E., Xu, Jianchu, and Doilom, Mingkwan

Published
2019
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46. Molecular taxonomy

Author

MMB, MMB Medische Staf, Hospenthal, Duane R., Rinaldi, Michael G., Walsh, Thomas J., Hagen, Ferry, Walther, Grit, Houbraken, Jos, Scott, James, Summerbell, Richard, Boekhout, Teun, MMB, MMB Medische Staf, Hospenthal, Duane R., Rinaldi, Michael G., Walsh, Thomas J., Hagen, Ferry, Walther, Grit, Houbraken, Jos, Scott, James, Summerbell, Richard, and Boekhout, Teun

Published
2023

47. Domestication in dry-cured meat Penicillium fungi : convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision

Author

Lo, Ying-Chu, Bruxaux, Jade, Rodríguez de la Vega, Ricardo C., O'Donnell, Samuel, Snirc, Alodie, Coton, Monika, Le Piver, Mélanie, Le Prieur, Stéphanie, Roueyre, Daniel, Dupont, Joëlle, Houbraken, Jos, Debuchy, Robert, Ropars, Jeanne, Giraud, Tatiana, Branca, Antoine, Lo, Ying-Chu, Bruxaux, Jade, Rodríguez de la Vega, Ricardo C., O'Donnell, Samuel, Snirc, Alodie, Coton, Monika, Le Piver, Mélanie, Le Prieur, Stéphanie, Roueyre, Daniel, Dupont, Joëlle, Houbraken, Jos, Debuchy, Robert, Ropars, Jeanne, Giraud, Tatiana, and Branca, Antoine

Abstract

Some fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers (HGTs). Studying their adaptation to human-made substrates is of fundamental and applied importance for understanding adaptation processes and for further strain improvement. We studied here the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense, the most common species in the dry-cured meat food industry, and P. salamii, used locally by farms. Both species displayed low genetic diversity, lacking differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild conspecifics, and those of P. nalgiovense were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed HGTs, particularly between P. nalgiovense and P. salamii (representing almost 1.5 Mb of cumulative length). HGTs additionally involved P. biforme, also found in dry-cured meat products. We further detected positive selection based on amino acid changes. Our findings suggest that selection by humans has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii, P. nalgiovense and P. biforme, indicating convergent adaptation to the same human-made environment. Our findings have implications for fundamental knowledge on adaptation and for the food industry: the discovery of dif

Published
2023
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49. IMA genome-F18: The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, 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, Wingfield, Brenda D., 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

50. Novel Antifungals and Aspergillus Section Terrei with Potpourri Susceptibility Profiles to Conventional Antifungals

Author

Vahedi-Shahandashti, Roya, Houbraken, Jos, Birch, Mike, Lass-Flörl, Cornelia, Vahedi-Shahandashti, Roya, Houbraken, Jos, Birch, Mike, and Lass-Flörl, Cornelia

Abstract

The epidemiology of invasive fungal infections (IFIs) is currently changing, driven by aggressive immunosuppressive therapy, leading to an expanded spectrum of patients at risk of IFIs. Aspergillosis is a leading cause of IFIs, which usually affects immunocompromised patients. There are a limited number of antifungal medications available for treating IFIs, and their effectiveness is often hindered by rising resistance rates and practical limitations. Consequently, new antifungals, especially those with novel mechanisms of action, are increasingly required. This study assessed the activity of four novel antifungal agents with different mechanisms of activity, namely, manogepix, rezafungin, ibrexafungerp, and olorofim, against 100 isolates of Aspergillus section Terrei, containing amphotericin-B (AmB)-wildtype/non-wildtype and azole-susceptible/-resistant strains, according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) method. In general, all tested agents showed potent and consistent activity against the tested isolates, exhibiting geometric mean (GM) and minimum effective concentration (MEC)/minimum inhibitory concentration (MIC) ranges, respectively, as follows: manogepix (0.048 mg/L, 0.032–0.5 mg/L), rezafungin (0.020 mg/L, 0.016–0.5 mg/L), ibrexafungerp (0.071 mg/L, 0.032–2 mg/L), and olorofim (0.008 mg/L, 0.008–0.032 mg/L). In terms of MIC90/MEC90, olorofim had the lowest values (0.008 mg/L), followed by rezafungin (0.032 mg/L), manogepix (0.125 mg/L), and ibrexafungerp (0.25 mg/L). All the antifungals tested demonstrated promising in vitro activity against Aspergillus section Terrei, including A. terreus as well as azole-resistant and AmB-non-wildtype cryptic species.

Published
2023

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