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

Ronald P. De Vries; Robert Riley; Ad Wiebenga; Guillermo Aguilar-Osorio; Sotiris Amillis; Cristiane Akemi Uchima; Gregor Anderluh; Mojtaba Asadollahi; Marion Askin; Kerrie Barry; Evy Battaglia; Tiziano Benocci; Susanna A. Braus-Stromeyer; Camila Caldana; David Canovas; Gustavo C. Cerqueira; Fusheng Chen; Wanping Chen; Cindy Choi; Alicia Clum; Renato Augusto Correa Dos Santos; Andre Ricardo De Lima Damasio; George Diallinas; Tamas Emri; Erzsébet Fekete; Michel Flipphi; Susanne Freyberg; Antonia Gallo; Christos Gournas; Rob Habgood; Matthieu Hainaut; Maria Laura Harispe; Bernard Henrissat; Kristiina S. Hilden; Ryan Hope; Abeer Hossain; Eugenia Karabika; Levente Karaffa; Zsolt Karanyi; Nada Krasevec; Alan Kuo; Harald Kusch; Kurt Labutti; Ellen L. Lagendijk; Alla Lapidus; Anthony Levasseur; Erika Lindquist; Anna Lipzen; Antonio F. Logrieco; Andrew Maccabe; Miia R. Makela; Iran Malavazi; Petter Melin; Vera Meyer; Natalia Mielnichuk; Marton Miskei; Akos P. Molnar; Giuseppina Mulé; Chew Yee Ngan; Margarita Orejas; Erzsebet Orosz; Jean Paul Ouedraogo; Karin M. Overkamp; Hee-Soo Park; Giancarlo Perrone; François Piumi; Peter J. Punt; Arthur F. J. Ram; Ana Ramón; Stefan Rauscher; Eric Record; Diego Mauricio Riaño-Pachón; Vincent Robert; Julian Roehrig; Roberto Ruller; Asaf Salamov; Nadhira S. Salih; Rob A. Samson; Erzsébet Sándor; Manuel Sanguinetti; Tabea Schutze; Kristina Sepcic; Ekaterina Shelest; Gavin Sherlock; Vicky Sophianopoulou; Fabiom. Squina; Hui Sun; Antonia Susca; Richard B. Todd; Adrian Tsang; 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; Mikael R. Andersen; David B. Archer; Scott E. Baker; Isabelle Benoit; Axel A. Brakhage; Gerhard H. Braus; Reinhard Fischer; Jens C. Frisvad; Gustavo H. Goldman; Jos Houbraken; Berl Oakley; Istvan Pocsi; Claudio Scazzocchio; Bernhard Seiboth; Patricia A. Vankuyk; Jennifer Wortman; Paul S. Dyer; Igor V. Grigoriev

doi:10.1186/s13059-017-1151-0

Journal Articles Genome Biology Year : 2017

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

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Ronald P. De Vries

Function : Author

Robert Riley

Function : Author

US Department of Energy Joint Genome Institute, Walnut Creek CA, USA

Ad Wiebenga

Function : Author

Fungal Physiology, CBS‑KNAW Fungal Biodiversity Centre and Fungal

Guillermo Aguilar-Osorio

Function : Author

Sotiris Amillis

Function : Author

Cristiane Akemi Uchima

Function : Author

Gregor Anderluh

Function : Author

Department for Molecular Biology and Nanobiotechnology

Mojtaba Asadollahi

Function : Author

Marion Askin

Function : Author

Kerrie Barry

Function : Author
PersonId : 776761
ORCID : 0000-0002-8999-6785

United States Department of Energy

Evy Battaglia

Function : Author

Microbiology and Kluyver Centre for Genomics of Industrial Fermentation

Fungal Physiology, CBS‑KNAW Fungal Biodiversity Centre and Fungal

Tiziano Benocci

Function : Author

Susanna A. Braus-Stromeyer

Function : Author

Camila Caldana

Function : Author

David Canovas

Function : Author

Gustavo C. Cerqueira

Function : Author

Fusheng Chen

Function : Author

Centre for Research in Neurodegenerative Diseases

Wanping Chen

Function : Author

Cindy Choi

Function : Author

US Department of Energy Joint Genome Institute

Alicia Clum

Function : Author

US Department of Energy Joint Genome Institute

Renato Augusto Correa Dos Santos

Function : Author

Andre Ricardo De Lima Damasio

Function : Author

George Diallinas

Function : Author

Faculty of Biology, University of Athens, Panepistimioupolis

Tamas Emri

Function : Author

Erzsébet Fekete

Function : Author

Dept. of Biochemical Engineering

Michel Flipphi

Function : Author

Dept. of Biochemical Engineering

Susanne Freyberg

Function : Author

Antonia Gallo

Function : Author

Christos Gournas

Function : Author

Rob Habgood

Function : Author

Matthieu Hainaut

Function : Author

Architecture et fonction des macromolécules biologiques

Maria Laura Harispe

Function : Author

Bernard Henrissat

Function : Author
PersonId : 833340

Architecture et fonction des macromolécules biologiques

Kristiina S. Hilden

Function : Author

Ryan Hope

Function : Author

Abeer Hossain

Function : Author

Eugenia Karabika

Function : Author

Levente Karaffa

Function : Author

Dept. of Biochemical Engineering

Zsolt Karanyi

Function : Author

Nada Krasevec

Function : Author

Alan Kuo

Function : Author
PersonId : 770173
ORCID : 0000-0003-3514-3530

Joint Genome Institute

Harald Kusch

Function : Author

Kurt Labutti

Function : Author
PersonId : 758166
ORCID : 0000-0002-5838-1972

United States Department of Energy

Ellen L. Lagendijk

Function : Author

Alla Lapidus

Function : Author

United States Department of Energy

Anthony Levasseur

Function : Author

Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes

Institut Hospitalier Universitaire Méditerranée Infection

Erika Lindquist

Function : Author

Department of Energy / Joint Genome Institute

Anna Lipzen

Function : Author
PersonId : 773817
ORCID : 0000-0003-2293-9329

US Department of Energy Joint Genome Institute, Walnut Creek CA, USA

Antonio F. Logrieco

Function : Author

Andrew Maccabe

Function : Author

Miia R. Makela

Function : Author

Helsingin yliopisto = Helsingfors universitet = University of Helsinki

Iran Malavazi

Function : Author

Petter Melin

Function : Author

Vera Meyer

Function : Author

Department of Molecular Microbiology and Biotechnology

The Netherlands & Kluyver Centre for Genomics of Industrial Fermentation

Natalia Mielnichuk

Function : Author

Marton Miskei

Function : Author

Akos P. Molnar

Function : Author

Giuseppina Mulé

Function : Author

Institute of Sciences of Food Production

Chew Yee Ngan

Function : Author

Margarita Orejas

Function : Author

Erzsebet Orosz

Function : Author

Jean Paul Ouedraogo

Function : Author

Karin M. Overkamp

Function : Author

Hee-Soo Park

Function : Author

Giancarlo Perrone

Function : Author

Institute of Sciences of Food Production

François Piumi

Function : Author
PersonId : 748553
IdHAL : francois-piumi
ORCID : 0000-0001-6036-7662

Biologie du Développement et Reproduction

Peter J. Punt

Function : Author

Arthur F. J. Ram

Function : Author

Department of Molecular Microbiology and Biotechnology

Ana Ramón

Function : Author

Sección Bioquímica, Depto. de Biología Celular y Molecular

Stefan Rauscher

Function : Author

Eric Record

Function : Author
PersonId : 736772
IdHAL : eric-record
ORCID : 0000-0002-7545-9997
IdRef : 168826275

Polytech Marseille

Biodiversité et Biotechnologie Fongiques

Diego Mauricio Riaño-Pachón

Function : Author

University of Potsdam = Universität Potsdam

Vincent Robert

Function : Author
PersonId : 3070
IdHAL : vincent-robert
ORCID : 0000-0002-4517-5213
IdRef : 161739083

Institut Polytechnique des Sciences Avancées

Institut de Mécanique Céleste et de Calcul des Ephémérides

Julian Roehrig

Function : Author

Roberto Ruller

Function : Author

Asaf Salamov

Function : Author

US Department of Energy Joint Genome Institute

Nadhira S. Salih

Function : Author

Rob A. Samson

Function : Author

Erzsébet Sándor

Function : Author

Department of Plant Protection

Manuel Sanguinetti

Function : Author

Sección Bioquímica, Depto. de Biología Celular y Molecular

Tabea Schutze

Function : Author

Kristina Sepcic

Function : Author

Ekaterina Shelest

Function : Author

Gavin Sherlock

Function : Author

Stanford University

Vicky Sophianopoulou

Function : Author

Fabiom. Squina

Function : Author

Hui Sun

Function : Author

United States Department of Energy

Antonia Susca

Function : Author

Istituto Scienze delle Produzioni Alimentari

Richard B. Todd

Function : Author

Adrian Tsang

Function : Author

Centre for Structural and Functional Genomics

Shiela E. Unkles

Function : Author

Nathalie van De Wiele

Function : Author

Diana Van Rossen-Uffink

Function : Author

Juliana Velasco De Castro Oliveira

Function : Author

Tammi C. Vesth

Function : Author

Jaap Visser

Function : Author

Jae-Hyuk Yu

Function : Author

Miaomiao Zhou

Function : Author

Fungal Physiology, CBS‑KNAW Fungal Biodiversity Centre and Fungal

Mikael R. Andersen

Function : Author

David B. Archer

Function : Author

School of Life Sciences

Scott E. Baker

Function : Author

Isabelle Benoit

Function : Author

Microbiology and Kluyver Centre for Genomics of Industrial Fermentation

Fungal Physiology, CBS‑KNAW Fungal Biodiversity Centre and Fungal

Axel A. Brakhage

Function : Author

Gerhard H. Braus

Function : Author

Reinhard Fischer

Function : Author

Jens C. Frisvad

Function : Author

Dept Syst Biol

Gustavo H. Goldman

Function : Author

Jos Houbraken

Function : Author

Fungal Physiology, CBS‑KNAW Fungal Biodiversity Centre and Fungal

Berl Oakley

Function : Author

Istvan Pocsi

Function : Author

Claudio Scazzocchio

Function : Author

Institut de Biologie Intégrative de la Cellule

Departement of Microbiology

Bernhard Seiboth

Function : Author

Research division biotechnology and microbiology

Patricia A. Vankuyk

Function : Author

Jennifer Wortman

Function : Author

Broad Institute of MIT and Harvard

Paul S. Dyer

Function : Author

School of Biology

Igor V. Grigoriev

Function : Author

US Department of Energy Joint Genome Institute, Walnut Creek CA, USA

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.

Keywords

Genome sequencing Comparative genomics Fungal biology

aspergillus champignon séquençage du génome génomique comparative biodiversité fongique

Domains

Infectious diseases

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https://hal.science/hal-01496186

Submitted on : Tuesday, September 26, 2017-10:19:53 PM

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hal-01496186 , version 1 (26-09-2017)

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HAL Id : hal-01496186 , version 1
DOI : 10.1186/s13059-017-1151-0
PRODINRA : 389512
PUBMED : 28196534
WOS : 000394827800001

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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, 2017, 18, ⟨10.1186/s13059-017-1151-0⟩. ⟨hal-01496186⟩

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

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