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


de Vries, Ronald and Riley, Robert and Wiebenga, Ad and Aguilar-Osorio, Guillermo and Amillis, Sotiris and Akemi Uchima, Cristiane and Anderluh, Gregor and Asadollahi, Mojtaba and Askin, Marion and Barry, Kerrie and Battaglia, Evy and Bayram, Ozgur and Benocci, Tiziano and Braus-Stromeyer, Susanna A. and Caldana, Camila and Canovas, David and Cerqueira, Gustavo C. and Chen, Fusheng and Chen, Wanping and Choi, Cindy and Clum, Alicia and Correa dos Santos, Renato Augusto and de Lima Damasio, Andre Ricardo and Diallinas, George and Emri, Tamas and Fekete, Erzsebet and Flipphi, Michel and Freyberg, Susanne and Gallo, Antonia and Gournas, Christos and Habgood, Rob and Hainaut, Matthieu and Harispe, Maria Laura and Henrissat, Bernard and Hilden, Kristiina S. and Hope, Ryan and Hossain, Abeer and Karabika, Eugenia and Karaffa, Levente and Karanyi, Zsolt and Krasevec, Nada and Kuo, Alan and Kusch, Harald and LaButti, Kurt and Lagendijk, Ellen L. and Lapidus, Alla and Levasseur, Anthony and Lindquist, Erika and Lipzen, Anna and Logrieco, Antonio F. and MacCabe, Andrew and Makela, Miia R. and Malavazi, Iran and Melin, Petter and Meyer, Vera and Mielnichuk, Natalia and Miskei, Marton and Molnar, Akos P. and Mule, Giuseppina and Ngan, Chew Yee and Orejas, Margarita and Orosz, Erzsebet and Ouedraogo, Jean Paul and Overkamp, Karin M. and Park, Hee-Soo and Perrone, Giancarlo and Piumi, Francois and Punt, Peter J. and Ram, Arthur F.J. and Ramon, Ana and Rauscher, Stefan and Record, Eric and Riano-Pachon, Diego Mauricio and Robert, Vincent and Rohrig, Julian and Ruller, Roberto and Salamov, Asaf and Salih, Nadhira S. and Samson, Rob A. and Sandor, Erzsebet and Sanguinetti, Manuel and Schutze, Tabea and Sepcic, Kristina and Shelest, Ekaterina and Sherlock, Gavin and Sophianopoulou, Vicky and Squina, Fabio M. and Sun, Hui and Susca, Antonia and Todd, Richard B. and Tsang, Adrian and Unkles, Sheila E. and van de Wiele, Nathalie and van Rossen-Uffink, Diana and Velasco de Castro Oliveria, Juliana and Vesth, Tammi C. and Visser, Jaap and Yu, Jae-Hyuk and Zhou, Miamiao and Andersen, Mikael R. and Archer, David B. and Baker, Scott E. and Benoit, Isabelle and Brakhage, Axel A. and Braus, Gerhard and Fischer, Reinhard and Frisvad, Jens C. and Goldman, Gustavo H. and Houbraken, Jos and Oakley, Berl and Pocsi, Istvan and Scazzocchio, Claudio and Seiboth, Bernhard and vanKuyk, Patricia A. and Wortman, Jennifer and 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, 18 (1). pp. 1-45. ISSN 1465-6906

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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.

Item Type: Article
Keywords: Aspergillus; Genome sequencing; Comparative genomics; Fungal biology;
Academic Unit: Faculty of Science and Engineering > Biology
Faculty of Science and Engineering > Research Institutes > Institute of Immunology
Item ID: 8153
Identification Number: 10.1186/s13059-017-1151-0
Depositing User: Ozgur Bayram
Date Deposited: 12 Apr 2017 10:34
Journal or Publication Title: Genome Biology
Publisher: BioMed Central
Refereed: Yes
URI:

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