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

Vries, Ronald P. de; Riley, Robert; Wiebenga, Ad; Aguilar-Osorio, Guillermo; Amillis, Sotiris; Akemi Uchima, Cristiane; Anderluh, Gregor; Asaollahi, Mojtaba; Askin, Marion; Barry, Kerrie; Battaglia, Evy; Bayram, Ozgur; Benocci, Tiziano; Braus-Stromeyer, Susanna A.; Caldana, Camila; Cánovas, David; Cerqueira, Gustavo C.; Chen, Fusheng; Chen, Wanping; Choi, Cindy; Clum, Alicia; Corrêa dos Santos, Renato Augusto; Lima Damásio, André Ricardo de; Diallinas, George; Emri, Tamás; Fekete, Erzébet; Flipphi, Michel; Freyburg, Susanne; Gallo, Antonia; Gournas, Christos; Habgood, Rob; Hainaut, Matthieu; Harispe, Maria Laura; Henrissat, Bernard; Hildén, 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; Mäkela, Miia R.; Malavazi, Iran; Melin, Petter; Meyer, Vera; Mielnichuk, Natalia; Miskei, Márton; Molnár, Ákos P.; Mulé, Giuseppina; Ngan, Chew Yee; Orejas, Margarita; Orosz, Erzsébet; 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; Riaño-Pachón, Diego Mauricio; Robert, Vincent; Röhrig, Julian; Ruller, Roberto; Salamov, Asaf; Salih, Nadhira S.; Samson, Rob A.; Sándor, Erzsébet; Sanguinetti, Manuel; Schütze, Tabea; Sepčić, Kristina; Shelest, Ekaterina; Sherlock, Gavin; Sophianopoulou, Vicky; Squina, Fabio M.; Sun, Hui; Susca, Antonia; Todd, Richard B.; Tsang, Adrian; Unkles, Shiela E.; Wiele, Nathalie van de; Rossen-Uffink, Diana van; Velasco de Castro Oliveira, Juliana; Vesth, Tammi C.; Visser, Jaap; Yu, Jae-Hyuk; Zhou, Miaomiao; Andersen, Mikael R.

Authors

Ronald P. de Vries

Robert Riley

Ad Wiebenga

Guillermo Aguilar-Osorio

Sotiris Amillis

Cristiane Akemi Uchima

Gregor Anderluh

Mojtaba Asaollahi

Marion Askin

Kerrie Barry

Evy Battaglia

Ozgur Bayram

Tiziano Benocci

Susanna A. Braus-Stromeyer

Camila Caldana

David Cánovas

Gustavo C. Cerqueira

Fusheng Chen

Wanping Chen

Cindy Choi

Alicia Clum

Renato Augusto Corrêa dos Santos

André Ricardo de Lima Damásio

George Diallinas

Tamás Emri

Erzébet Fekete

Michel Flipphi

Susanne Freyburg

Antonia Gallo

Christos Gournas

Rob Habgood

Matthieu Hainaut

Maria Laura Harispe

Bernard Henrissat

Kristiina S. Hildén

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. Mäkela

Iran Malavazi

Petter Melin

Vera Meyer

Natalia Mielnichuk

Márton Miskei

Ákos P. Molnár

Giuseppina Mulé

Chew Yee Ngan

Margarita Orejas

Erzsébet Orosz

Jean Paul Ouedraogo

Karin M. Overkamp

Hee-Soo Park

Giancarlo Perrone

Francois Piumi

Peter J. Punt

Arthur F.J. Ram

Ana Ramon

Stefan Rauscher

Eric Record

Diego Mauricio Riaño-Pachón

Vincent Robert

Julian Röhrig

Roberto Ruller

Asaf Salamov

Nadhira S. Salih

Rob A. Samson

Erzsébet Sándor

Manuel Sanguinetti

Tabea Schütze

Kristina Sepčić

Ekaterina Shelest

Gavin Sherlock

Vicky Sophianopoulou

Fabio M. 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



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.

Journal Article Type Article
Publication Date Feb 14, 2017
Journal Genome Biology
Print ISSN 1474-760X
Electronic ISSN 1474-760X
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 18
Article Number 28
APA6 Citation Vries, R. P. D., Riley, R., Wiebenga, A., Aguilar-Osorio, G., Amillis, S., Akemi Uchima, C., …Grigoriev, I. V. (2017). Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biology, 18, doi:10.1186/s13059-017-1151-0. ISSN 1474-760X
DOI https://doi.org/10.1186/s13059-017-1151-0
Keywords Genome sequencing, Comparative genomics, Fungal biology
Publisher URL https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1151-0
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0
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Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0





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