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
Sequencing fungal genomes has now become very common and the list of genomes in this manuscript reflects this. Particularly relevant is that the first announcement is a re-identification of Penicillium genomes available on NCBI. The fact that more than 100 of these genomes have been deposited without the correct species names speak volumes to the fact that we must continue training fungal taxonomists and the importance of the International Mycological Association (after which this journal is named). When we started the genome series in 2013, one of the essential aspects was the need to have a phylogenetic tree as part of the manuscript. This came about as the result of a discussion with colleagues in NCBI who were trying to deal with the very many incorrectly identified bacterial genomes (at the time) which had been submitted to NCBI. We are now in the same position with fungal genomes. Sequencing a fungal genome is all too easy but providing a correct species name and ensuring that the fungus has in fact been correctly identified seems to be more difficult. We know that there are thousands of fungi which have not yet been described. The availability of sequence data has made identification of fungi easier but also serves to highlight the need to have a fungal taxonomist in the project to make sure that mistakes are not made.
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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2023-10-06
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Online Access: | http://hdl.handle.net/10261/347787 http://dx.doi.org/10.13039/501100001321 http://dx.doi.org/10.13039/100000015 http://dx.doi.org/10.13039/501100008775 https://api.elsevier.com/content/abstract/scopus_id/85173698663 |
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Sequencing fungal genomes has now become very common and the list of genomes in this manuscript reflects this. Particularly relevant is that the first announcement is a re-identification of Penicillium genomes available on NCBI. The fact that more than 100 of these genomes have been deposited without the correct species names speak volumes to the fact that we must continue training fungal taxonomists and the importance of the International Mycological Association (after which this journal is named). When we started the genome series in 2013, one of the essential aspects was the need to have a phylogenetic tree as part of the manuscript. This came about as the result of a discussion with colleagues in NCBI who were trying to deal with the very many incorrectly identified bacterial genomes (at the time) which had been submitted to NCBI. We are now in the same position with fungal genomes. Sequencing a fungal genome is all too easy but providing a correct species name and ensuring that the fungus has in fact been correctly identified seems to be more difficult. We know that there are thousands of fungi which have not yet been described. The availability of sequence data has made identification of fungi easier but also serves to highlight the need to have a fungal taxonomist in the project to make sure that mistakes are not made. |
author2 |
Ministry of Education, Youth and Sports (Czech Republic) |
author_facet |
Ministry of Education, Youth and Sports (Czech Republic) 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 Angelis, Maria de 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. |
format |
artículo |
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 Angelis, Maria de 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. |
spellingShingle |
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 Angelis, Maria de 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. 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_sort |
Visagie, Cobus M. |
title |
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 |
title_short |
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 |
title_full |
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 |
title_fullStr |
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 |
title_full_unstemmed |
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 |
title_sort |
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 |
publishDate |
2023-10-06 |
url |
http://hdl.handle.net/10261/347787 http://dx.doi.org/10.13039/501100001321 http://dx.doi.org/10.13039/100000015 http://dx.doi.org/10.13039/501100008775 https://api.elsevier.com/content/abstract/scopus_id/85173698663 |
work_keys_str_mv |
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imagenomef18thereidentificationofpenicilliumgenomesavailableinncbianddraftgenomesforpenicilliumspeciesfromdrycuredmeatpenicilliumbiformepbrevicompactumpsolitumandpcvjetkoviciipewenomyceskutranfypewlalenivorapewtapulicolapewkalosusteratosphaeriacarnegieian AT duongtuana imagenomef18thereidentificationofpenicilliumgenomesavailableinncbianddraftgenomesforpenicilliumspeciesfromdrycuredmeatpenicilliumbiformepbrevicompactumpsolitumandpcvjetkoviciipewenomyceskutranfypewlalenivorapewtapulicolapewkalosusteratosphaeriacarnegieian AT eichmeierales imagenomef18thereidentificationofpenicilliumgenomesavailableinncbianddraftgenomesforpenicilliumspeciesfromdrycuredmeatpenicilliumbiformepbrevicompactumpsolitumandpcvjetkoviciipewenomyceskutranfypewlalenivorapewtapulicolapewkalosusteratosphaeriacarnegieian AT gramajedavid 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1816138737805950976 |
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dig-icvv-es-10261-3477872024-10-28T21:41:03Z 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 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 Angelis, Maria de 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. Ministry of Education, Youth and Sports (Czech Republic) Mendel University Department of Energy (US) Joint Genome Institute (US) Bioenergy Research Center (US) Department of Science and Innovation (South Africa) National Research Foundation (South Africa) Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] Sequencing fungal genomes has now become very common and the list of genomes in this manuscript reflects this. Particularly relevant is that the first announcement is a re-identification of Penicillium genomes available on NCBI. The fact that more than 100 of these genomes have been deposited without the correct species names speak volumes to the fact that we must continue training fungal taxonomists and the importance of the International Mycological Association (after which this journal is named). When we started the genome series in 2013, one of the essential aspects was the need to have a phylogenetic tree as part of the manuscript. This came about as the result of a discussion with colleagues in NCBI who were trying to deal with the very many incorrectly identified bacterial genomes (at the time) which had been submitted to NCBI. We are now in the same position with fungal genomes. Sequencing a fungal genome is all too easy but providing a correct species name and ensuring that the fungus has in fact been correctly identified seems to be more difficult. We know that there are thousands of fungi which have not yet been described. The availability of sequence data has made identification of fungi easier but also serves to highlight the need to have a fungal taxonomist in the project to make sure that mistakes are not made. Trichoderma atroviride SC1 genome sequencing was carried out at the Mendel University in Brno, Czech Republic, and was funded by the Ministerstvo Školství, Mládeže a Tělovýchovy (CZ.02.1.01/0.0/0.0/16_025/0007314) and by the Internal Grant of Mendel University in Brno, No. IGA-ZF/2021-SI2005. The work on Penicillium species from dry cured meat (proposal: 10.46936/10.25585/60001195) conducted by the US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337) proposal: 10.46936/10.25585/60001195; DOE BER Bioenergy Research Center, are supported by the Office of Science of the US Department of Energy operated under Contract No. DE-AC02-05CH11231. Funding for the project on the T. carnegiei and the Pewenomyces species genomes was provided by Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence in Plant Health Biotechnology (CPHB), South Africa and the DST-NRF SARChI chair in Fungal Genomics. Peer reviewed 2024-02-21T08:40:53Z 2024-02-21T08:40:53Z 2023-10-06 artículo http://purl.org/coar/resource_type/c_6501 IMA Fungus 14: 21 (2023) 2210-6359 http://hdl.handle.net/10261/347787 10.1186/s43008-023-00121-w http://dx.doi.org/10.13039/501100001321 http://dx.doi.org/10.13039/100000015 http://dx.doi.org/10.13039/501100008775 37803441 2-s2.0-85173698663 https://api.elsevier.com/content/abstract/scopus_id/85173698663 en Publisher's version The underlying dataset has been published as supplementary material of the article in the publisher platform at https://doi.org/10.1186/s43008-023-00121-w https://doi.org/10.1186/s43008-023-00121-w Sí open application/pdf |