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

Ronald P. 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 Özgür Bayram 6 Tiziano Benocci Susanna A. Braus-Stromeyer Camila Caldana David Canovas Gustavo C. Cerqueira Fusheng Chen 7 Wanping Chen Cindy Choi 8 Alicia Clum 8 Renato Augusto Santos Andre Ricardo Lima Damasio George Diallinas 9 Tamas Emri Erzsébet Fekete 10 Michel Flipphi 10 Susanne Freyberg Antonia Gallo Christos Gournas Rob Habgood Matthieu Hainaut 11 Maria Laura Harispe Bernard Henrissat 11 Kristiina S. Hilden Ryan Hope Abeer Hossain Eugenia Karabika Levente Karaffa 10 Zsolt Karanyi Nada Krasevec Alan Kuo 12 Harald Kusch Kurt Labutti 4 Ellen L. Lagendijk Alla Lapidus 4 Anthony Levasseur 13, 14 Erika Lindquist 15 Anna Lipzen 1 Antonio F. Logrieco Andrew Maccabe Miia R. Makela 16 Iran Malavazi Petter Melin Vera Meyer 17, 18 Natalia Mielnichuk Marton Miskei Akos P. Molnar Giuseppina Mulé 19 Chew Yee Ngan Margarita Orejas Erzsebet Orosz Jean Paul Ouedraogo Karin M. Overkamp Hee-Soo Park Giancarlo Perrone 19 François Piumi 20 Peter J. Punt Arthur F. J. Ram 17 Ana Ramón 21 Stefan Rauscher Eric Record 22, 23 Diego Mauricio Riaño-Pachón 24 Vincent Robert 25, 26 Julian Roehrig Roberto Ruller Asaf Salamov 8 Nadhira S. Salih Rob A. Samson Erzsébet Sándor 27 Manuel Sanguinetti 21 Tabea Schutze Kristina Sepcic Ekaterina Shelest Gavin Sherlock 28 Vicky Sophianopoulou Fabiom. Squina Hui Sun 4 Antonia Susca 29 Richard B. Todd Adrian Tsang 30 Shiela E. Unkles Nathalie Wiele Diana Rossen-Uffink Juliana Velasco Castro Oliveira Tammi C. Vesth Jaap Visser Jae-Hyuk Yu Miaomiao Zhou 2 Mikael R. Andersen David B. Archer 31 Scott E. Baker Isabelle Benoit 5, 2 Axel A. Brakhage Gerhard H. Braus Reinhard Fischer Jens C. Frisvad 32 Gustavo H. Goldman Jos Houbraken 2 Berl Oakley Istvan Pocsi Claudio Scazzocchio 33, 34 Bernhard Seiboth 35 Patricia A. Vankuyk Jennifer Wortman 36 Paul S. Dyer 37 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. 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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