Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

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de Vries, Ronald P. ; Riley, Robert ; Wiebenga, Ad ; Aguilar-Osorio, Guillermo ; Amillis, Sotiris ; Uchima, Cristiane Akemi ; Anderluh, Gregor ; Asadollahi, Mojtaba ; Askin, Marion ; Barry, Kerrie ; Battaglia, Evy ; Bayram, Ozgur ; Benocci, Tiziano ; Braus-Stromeyer, Susanna A. ; Caldana, Camila ; Canovas, David ; Cerqueira, Gustavo C. ; Chen, Fusheng ; Chen, Wanping ; Choi, Cindy ; Clum, Alicia ; Correa dos Santos, Renato Augusto ; de Lima Damasio, Andre Ricardo ; Diallinas, George ; Emri, Tamas ; Fekete, Erzsebet ; Flipphi, Michel ; Freyberg, Susanne ; Gallo, Antonia ; Gournas, Christos ; Habgood, Rob ; Hainaut, Matthieu ; Laura Harispe, Maria ; Henrissat, Bernard ; Hilden, 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 ; Makela, Miia R. ; Malavazi, Iran ; Melin, Petter ; Meyer, Vera ; Mielnichuk, Natalia ; Miskei, Marton ; Molnar, Akos P. ; Mule, Giuseppina ; Ngan, Chew Yee ; Orejas, Margarita ; Orosz, Erzsebet ; 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 ; Riano-Pachon, Diego Mauricio ; Robert, Vincent ; Roehrig, Julian ; Ruller, Roberto ; Salamov, Asaf ; Salih, Nadhira S. ; Samson, Rob A. ; Sandor, Erzsebet ; Sanguinetti, Manuel ; Schutze, Tabea ; Sepcic, Kristina ; Shelest, Ekaterina ; Sherlock, Gavin ; Sophianopoulou, Vicky ; Squina, FabioM. ; Sun, Hui ; Susca, Antonia ; Todd, Richard B. ; Tsang, Adrian ; Unkles, Shiela E. ; van de Wiele, Nathalie ; van Rossen-Uffink, Diana ; de Castro Oliveira, Juliana Velasco ; 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 ; Pocsi, Istvan ; Scazzocchio, Claudio ; Seiboth, Bernhard ; vanKuyk, Patricia A. ; Wortman, Jennifer ; Dyer, Paul S. ; Grigoriev, Igor V.

• Document type: Journal article
• Source: Genome Biology; v. 18, FEB 14 2017.
• Web of Science Citations: 108

Abstract

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. (AU)

• FAPESP's process: 14/06923-6 - Sugar cane biomass recalcitrance: basic knowledge related to the cell wall construction, pretreatment and enzymatic digestion, applied for the development of innovative biorefinery models
• Grantee: Andre Luis Ferraz
• Support type: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• FAPESP's process: 14/11766-7 - Characterization of novel transcription factors of Trichoderma reesei involved in the degradation of lignocellulosic biomass
• Grantee: Juliana Velasco de Castro Oliveira
• Support type: Program for Research on Bioenergy (BIOEN) - Regular Program Grants
• FAPESP's process: 11/08945-9 - Comparative genomic studies of global gene expression in filamentous fungi grown on bagasse and sugarcane culm
• Grantee: Juliana Velasco de Castro Oliveira
• Support type: Regular Research Grants
• FAPESP's process: 14/10351-8 - Phenotype characterization of Neurospora crassa deletion strains grown on Avicel and sugarcane bagasse
• Grantee: Cristiane Akemi Uchima
• Support type: Scholarships abroad - Research Internship - Post-doctor
• FAPESP's process: 12/19040-0 - Characterization of gene expression of Neurospora crassa in response to deconstruction of sugar cane bagasse
• Grantee: Cristiane Akemi Uchima
• Support type: Scholarships in Brazil - Post-Doctorate
• FAPESP's process: 12/20549-4 - Secretion of heterologous glycoproteins in Aspergillus: effect of glycosylation pattern in functional parameters of glycosyl hydrolases
• Grantee: André Ricardo de Lima Damasio
• Support type: Program for Research on Bioenergy (BIOEN) - Young Investigators Grants