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

Ronald P. De Vries Robert Riley 1 Ad Wiebenga 2 Guillermo Aguilar-Osorio Sotiris Amillis Cristiane Akemi Uchima Gregor Anderluh 3 Mojtaba Asadollahi Marion Askin Kerrie Barry 4 Evy Battaglia 5, 2 Tiziano Benocci Susanna A. Braus-Stromeyer Camila Caldana David Canovas Gustavo C. Cerqueira Fusheng Chen 6 Wanping Chen Cindy Choi 7 Alicia Clum 7 Renato Augusto Correa Dos Santos Andre Ricardo De Lima Damasio George Diallinas 8 Tamas Emri Erzsébet Fekete 9 Michel Flipphi 9 Susanne Freyberg Antonia Gallo Christos Gournas Rob Habgood Matthieu Hainaut 10 Maria Laura Harispe Bernard Henrissat 10 Kristiina S. Hilden Ryan Hope Abeer Hossain Eugenia Karabika Levente Karaffa 9 Zsolt Karanyi Nada Krasevec Alan Kuo 11 Harald Kusch Kurt Labutti 4 Ellen L. Lagendijk Alla Lapidus 4 Anthony Levasseur 12, 13 Erika Lindquist 14 Anna Lipzen 1 Antonio F. Logrieco Andrew Maccabe Miia R. Makela 15 Iran Malavazi Petter Melin Vera Meyer 16, 17 Natalia Mielnichuk Marton Miskei Akos P. Molnar Giuseppina Mulé 18 Chew yee Ngan Margarita Orejas Erzsebet Orosz Jean Paul Ouedraogo Karin M. Overkamp Hee-Soo Park Giancarlo Perrone 18 François Piumi 19 Peter J. Punt Arthur F. J. Ram 16 Ana Ramón 20 Stefan Rauscher Eric Record 21, 22 Diego Mauricio Riaño-Pachón 23 Vincent Robert 24, 25 Julian Roehrig Roberto Ruller Asaf Salamov 7 Nadhira S. Salih Rob A. Samson Erzsébet Sándor 26 Manuel Sanguinetti 20 Tabea Schutze Kristina Sepcic Ekaterina Shelest Gavin Sherlock 27 Vicky Sophianopoulou Fabiom. Squina Hui Sun 4 Antonia Susca 28 Richard B. Todd Adrian Tsang 29 Shiela E. Unkles Nathalie van De Wiele Diana Van Rossen-Uffink Juliana Velasco De Castro Oliveira Tammi C. Vesth Jaap Visser Jae-Hyuk yu Miaomiao Zhou 2 Mikael R. Andersen David B. Archer 30 Scott E. Baker Isabelle Benoit 5, 2 Axel A. Brakhage Gerhard H. Braus Reinhard Fischer Jens C. Frisvad 31 Gustavo H. Goldman Jos Houbraken 2 Berl Oakley Istvan Pocsi Claudio Scazzocchio 32, 33 Bernhard Seiboth 34 Patricia A. Vankuyk Jennifer Wortman 35 Paul S. Dyer 36 Igor V. Grigoriev 1 
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.
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Ronald P. De Vries, Robert Riley, Ad Wiebenga, Guillermo Aguilar-Osorio, Sotiris Amillis, et al.. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biology, BioMed Central, 2017, 18, ⟨10.1186/s13059-017-1151-0⟩. ⟨hal-01496186⟩



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