Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
Background: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight a...
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| Format: | Article |
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BioMed Central
2017
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| Subjects: | |
| Online Access: | https://eprints.nottingham.ac.uk/40582/ |
| _version_ | 1848796092203794432 |
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| author | Vries, Ronald P. de Riley, Robert Wiebenga, Ad Aguilar-Osorio, Guillermo Amillis, Sotiris Akemi Uchima, Cristiane Anderluh, Gregor Asaollahi, Mojtaba Askin, Marion Barry, Kerrie Battaglia, Evy Bayram, Ozgur Benocci, Tiziano Braus-Stromeyer, Susanna A. Caldana, Camila Cánovas, David Cerqueira, Gustavo C. Chen, Fusheng Chen, Wanping Choi, Cindy Clum, Alicia Corrêa dos Santos, Renato Augusto Lima Damásio, André Ricardo de Diallinas, George Emri, Tamás Fekete, Erzébet Flipphi, Michel Freyburg, Susanne Gallo, Antonia Gournas, Christos Habgood, Rob Hainaut, Matthieu Harispe, Maria Laura Henrissat, Bernard Hildén, Kristiina S. Hope, Ryan Hossain, Abeer Karabika, Eugenia Karaffa, Levente Karanyi, Zsolt Krasevec, Nada Kuo, Alan Kusch, Harald LaButti, Kurt Lagendijk, Ellen L. Lapidus, Alla Levasseur, Anthony Lindquist, Erika Lipzen, Anna Logrieco, Antonio F. MacCabe, Andrew Mäkela, Miia R. Malavazi, Iran Melin, Petter Meyer, Vera Mielnichuk, Natalia Miskei, Márton Molnár, Ákos P. Mulé, Giuseppina Ngan, Chew Yee Orejas, Margarita Orosz, Erzsébet Ouedraogo, Jean Paul Overkamp, Karin M. Park, Hee-Soo Perrone, Giancarlo Piumi, Francois Punt, Peter J. Ram, Arthur F.J. Ramon, Ana Rauscher, Stefan Record, Eric Riaño-Pachón, Diego Mauricio Robert, Vincent Röhrig, Julian Ruller, Roberto Salamov, Asaf Salih, Nadhira S. Samson, Rob A. Sándor, Erzsébet Sanguinetti, Manuel Schütze, Tabea Sepčić, Kristina Shelest, Ekaterina Sherlock, Gavin Sophianopoulou, Vicky Squina, Fabio M. Sun, Hui Susca, Antonia Todd, Richard B. Tsang, Adrian Unkles, Shiela E. Wiele, Nathalie van de Rossen-Uffink, Diana van Velasco de Castro Oliveira, Juliana Vesth, Tammi C. Visser, Jaap Yu, Jae-Hyuk Zhou, Miaomiao Andersen, Mikael R. Archer, David B. Baker, Scott E. Benoit, Isabelle Brakhage, Axel A. Braus, Gerhard H. Fischer, Reinhard Frisvad, Jens C. Goldman, Gustavo H. Houbraken, Jos Oakley, Berl Pócsi, István Scazzocchio, Claudio Seiboth, Bernhard vanKuyk, Patricia A. Wortman, Jennifer Dyer, Paul S. Grigoriev, Igor V. |
| author_facet | Vries, Ronald P. de Riley, Robert Wiebenga, Ad Aguilar-Osorio, Guillermo Amillis, Sotiris Akemi Uchima, Cristiane Anderluh, Gregor Asaollahi, Mojtaba Askin, Marion Barry, Kerrie Battaglia, Evy Bayram, Ozgur Benocci, Tiziano Braus-Stromeyer, Susanna A. Caldana, Camila Cánovas, David Cerqueira, Gustavo C. Chen, Fusheng Chen, Wanping Choi, Cindy Clum, Alicia Corrêa dos Santos, Renato Augusto Lima Damásio, André Ricardo de Diallinas, George Emri, Tamás Fekete, Erzébet Flipphi, Michel Freyburg, Susanne Gallo, Antonia Gournas, Christos Habgood, Rob Hainaut, Matthieu Harispe, Maria Laura Henrissat, Bernard Hildén, Kristiina S. Hope, Ryan Hossain, Abeer Karabika, Eugenia Karaffa, Levente Karanyi, Zsolt Krasevec, Nada Kuo, Alan Kusch, Harald LaButti, Kurt Lagendijk, Ellen L. Lapidus, Alla Levasseur, Anthony Lindquist, Erika Lipzen, Anna Logrieco, Antonio F. MacCabe, Andrew Mäkela, Miia R. Malavazi, Iran Melin, Petter Meyer, Vera Mielnichuk, Natalia Miskei, Márton Molnár, Ákos P. Mulé, Giuseppina Ngan, Chew Yee Orejas, Margarita Orosz, Erzsébet Ouedraogo, Jean Paul Overkamp, Karin M. Park, Hee-Soo Perrone, Giancarlo Piumi, Francois Punt, Peter J. Ram, Arthur F.J. Ramon, Ana Rauscher, Stefan Record, Eric Riaño-Pachón, Diego Mauricio Robert, Vincent Röhrig, Julian Ruller, Roberto Salamov, Asaf Salih, Nadhira S. Samson, Rob A. Sándor, Erzsébet Sanguinetti, Manuel Schütze, Tabea Sepčić, Kristina Shelest, Ekaterina Sherlock, Gavin Sophianopoulou, Vicky Squina, Fabio M. Sun, Hui Susca, Antonia Todd, Richard B. Tsang, Adrian Unkles, Shiela E. Wiele, Nathalie van de Rossen-Uffink, Diana van Velasco de Castro Oliveira, Juliana Vesth, Tammi C. Visser, Jaap Yu, Jae-Hyuk Zhou, Miaomiao Andersen, Mikael R. Archer, David B. Baker, Scott E. Benoit, Isabelle Brakhage, Axel A. Braus, Gerhard H. Fischer, Reinhard Frisvad, Jens C. Goldman, Gustavo H. Houbraken, Jos Oakley, Berl Pócsi, István Scazzocchio, Claudio Seiboth, Bernhard vanKuyk, Patricia A. Wortman, Jennifer Dyer, Paul S. Grigoriev, Igor V. |
| author_sort | Vries, Ronald P. de |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | Background: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus.
Results: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli.
Conclusions: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi. |
| first_indexed | 2025-11-14T19:42:29Z |
| format | Article |
| id | nottingham-40582 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:42:29Z |
| publishDate | 2017 |
| publisher | BioMed Central |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-405822020-05-04T18:31:20Z https://eprints.nottingham.ac.uk/40582/ Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus Vries, Ronald P. de Riley, Robert Wiebenga, Ad Aguilar-Osorio, Guillermo Amillis, Sotiris Akemi Uchima, Cristiane Anderluh, Gregor Asaollahi, Mojtaba Askin, Marion Barry, Kerrie Battaglia, Evy Bayram, Ozgur Benocci, Tiziano Braus-Stromeyer, Susanna A. Caldana, Camila Cánovas, David Cerqueira, Gustavo C. Chen, Fusheng Chen, Wanping Choi, Cindy Clum, Alicia Corrêa dos Santos, Renato Augusto Lima Damásio, André Ricardo de Diallinas, George Emri, Tamás Fekete, Erzébet Flipphi, Michel Freyburg, Susanne Gallo, Antonia Gournas, Christos Habgood, Rob Hainaut, Matthieu Harispe, Maria Laura Henrissat, Bernard Hildén, Kristiina S. Hope, Ryan Hossain, Abeer Karabika, Eugenia Karaffa, Levente Karanyi, Zsolt Krasevec, Nada Kuo, Alan Kusch, Harald LaButti, Kurt Lagendijk, Ellen L. Lapidus, Alla Levasseur, Anthony Lindquist, Erika Lipzen, Anna Logrieco, Antonio F. MacCabe, Andrew Mäkela, Miia R. Malavazi, Iran Melin, Petter Meyer, Vera Mielnichuk, Natalia Miskei, Márton Molnár, Ákos P. Mulé, Giuseppina Ngan, Chew Yee Orejas, Margarita Orosz, Erzsébet Ouedraogo, Jean Paul Overkamp, Karin M. Park, Hee-Soo Perrone, Giancarlo Piumi, Francois Punt, Peter J. Ram, Arthur F.J. Ramon, Ana Rauscher, Stefan Record, Eric Riaño-Pachón, Diego Mauricio Robert, Vincent Röhrig, Julian Ruller, Roberto Salamov, Asaf Salih, Nadhira S. Samson, Rob A. Sándor, Erzsébet Sanguinetti, Manuel Schütze, Tabea Sepčić, Kristina Shelest, Ekaterina Sherlock, Gavin Sophianopoulou, Vicky Squina, Fabio M. Sun, Hui Susca, Antonia Todd, Richard B. Tsang, Adrian Unkles, Shiela E. Wiele, Nathalie van de Rossen-Uffink, Diana van Velasco de Castro Oliveira, Juliana Vesth, Tammi C. Visser, Jaap Yu, Jae-Hyuk Zhou, Miaomiao Andersen, Mikael R. Archer, David B. Baker, Scott E. Benoit, Isabelle Brakhage, Axel A. Braus, Gerhard H. Fischer, Reinhard Frisvad, Jens C. Goldman, Gustavo H. Houbraken, Jos Oakley, Berl Pócsi, István Scazzocchio, Claudio Seiboth, Bernhard vanKuyk, Patricia A. Wortman, Jennifer Dyer, Paul S. Grigoriev, Igor V. Background: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. Results: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. Conclusions: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi. BioMed Central 2017-01-09 Article PeerReviewed Vries, Ronald P. de, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Akemi Uchima, Cristiane, Anderluh, Gregor, Asaollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Cánovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Corrêa dos Santos, Renato Augusto, Lima Damásio, André Ricardo de, Diallinas, George, Emri, Tamás, Fekete, Erzébet, Flipphi, Michel, Freyburg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hildén, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio F., MacCabe, Andrew, Mäkela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P., Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean Paul, Overkamp, Karin M., Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J., Ram, Arthur F.J., Ramon, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio M., Sun, Hui, Susca, Antonia, Todd, Richard B., Tsang, Adrian, Unkles, Shiela E., Wiele, Nathalie van de, Rossen-Uffink, Diana van, Velasco de Castro Oliveira, Juliana, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, Andersen, Mikael R., Archer, David B., Baker, Scott E., Benoit, Isabelle, Brakhage, Axel A., Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A., Wortman, Jennifer, Dyer, Paul S. and Grigoriev, Igor V. (2017) Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biology . ISSN 1474-760X (Unpublished) Genome sequencing Comparative genomics Fungal biology doi:10.1186/s13059-017-1151-0 doi:10.1186/s13059-017-1151-0 |
| spellingShingle | Genome sequencing Comparative genomics Fungal biology Vries, Ronald P. de Riley, Robert Wiebenga, Ad Aguilar-Osorio, Guillermo Amillis, Sotiris Akemi Uchima, Cristiane Anderluh, Gregor Asaollahi, Mojtaba Askin, Marion Barry, Kerrie Battaglia, Evy Bayram, Ozgur Benocci, Tiziano Braus-Stromeyer, Susanna A. Caldana, Camila Cánovas, David Cerqueira, Gustavo C. Chen, Fusheng Chen, Wanping Choi, Cindy Clum, Alicia Corrêa dos Santos, Renato Augusto Lima Damásio, André Ricardo de Diallinas, George Emri, Tamás Fekete, Erzébet Flipphi, Michel Freyburg, Susanne Gallo, Antonia Gournas, Christos Habgood, Rob Hainaut, Matthieu Harispe, Maria Laura Henrissat, Bernard Hildén, Kristiina S. Hope, Ryan Hossain, Abeer Karabika, Eugenia Karaffa, Levente Karanyi, Zsolt Krasevec, Nada Kuo, Alan Kusch, Harald LaButti, Kurt Lagendijk, Ellen L. Lapidus, Alla Levasseur, Anthony Lindquist, Erika Lipzen, Anna Logrieco, Antonio F. MacCabe, Andrew Mäkela, Miia R. Malavazi, Iran Melin, Petter Meyer, Vera Mielnichuk, Natalia Miskei, Márton Molnár, Ákos P. Mulé, Giuseppina Ngan, Chew Yee Orejas, Margarita Orosz, Erzsébet Ouedraogo, Jean Paul Overkamp, Karin M. Park, Hee-Soo Perrone, Giancarlo Piumi, Francois Punt, Peter J. Ram, Arthur F.J. Ramon, Ana Rauscher, Stefan Record, Eric Riaño-Pachón, Diego Mauricio Robert, Vincent Röhrig, Julian Ruller, Roberto Salamov, Asaf Salih, Nadhira S. Samson, Rob A. Sándor, Erzsébet Sanguinetti, Manuel Schütze, Tabea Sepčić, Kristina Shelest, Ekaterina Sherlock, Gavin Sophianopoulou, Vicky Squina, Fabio M. Sun, Hui Susca, Antonia Todd, Richard B. Tsang, Adrian Unkles, Shiela E. Wiele, Nathalie van de Rossen-Uffink, Diana van Velasco de Castro Oliveira, Juliana Vesth, Tammi C. Visser, Jaap Yu, Jae-Hyuk Zhou, Miaomiao Andersen, Mikael R. Archer, David B. Baker, Scott E. Benoit, Isabelle Brakhage, Axel A. Braus, Gerhard H. Fischer, Reinhard Frisvad, Jens C. Goldman, Gustavo H. Houbraken, Jos Oakley, Berl Pócsi, István Scazzocchio, Claudio Seiboth, Bernhard vanKuyk, Patricia A. Wortman, Jennifer Dyer, Paul S. Grigoriev, Igor V. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus |
| title | Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus |
| title_full | Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus |
| title_fullStr | Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus |
| title_full_unstemmed | Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus |
| title_short | Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus |
| title_sort | comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus aspergillus |
| topic | Genome sequencing Comparative genomics Fungal biology |
| url | https://eprints.nottingham.ac.uk/40582/ https://eprints.nottingham.ac.uk/40582/ |