Agradecimentos: Members of the University of Debrecen were supported financially by the Hungarian Scientific Research Fund (grant K100464 to IP) as well as by the TÁMOP 4.2.1./B-09/1/KONV-2010-0007 and SROP-4.2.2.B-15/1/KONV-2015-0001 projects, which were supported by the European Union, co-financed by the European Social Fund. EO was a recipient of a Campus Hungary Programme scholarship to the CBS-KNAW Fungal Biodiversity Centre. The authors aknowledge support from the Federal Ministery of Education and Research (BMBF) BioFung and the Deutsche Forschungsgemeinschaft (DFG) to GB, ES, and AAB. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. FC was supported by the Major Program of National Natural Science Foundation of China (No. 31330059). WC was supported by the National Natural Science Foundation of China (No. 31601446) and the Fundamental Research Funds for the Central Universities (Nos. 2662014BQ051 and 2662015QC003). TB and IB were supported by grants of the Dutch Technology Foundation STW, Applied Science division of NWO, and the Technology Program of the Ministry of Economic Affairs UGC 14270 to RPdV. PAvK, MaA, and DvRU were supported by the Netherlands Technology Foundation STW (LGC 7393). We acknowledge financial support from the FWF (M01693-B22) to DCa. This work was in part supported by the Intelligent Synthetic Biology Center of Global Frontier Project (2011-0031955) funded by the Ministry of Education, Science and Technology grants to JHY and Science Foundation Ireland 13/CDA/2142 to OB. NS was supported by a scholarship from the Kurdistan Regional Government of Iraq. HSP was supported by the National Research Foundation of Korea (NRF) grant founded by the Korean Government (no. 2016010945). The work at UW-Madison (JHY) was supported by the Intelligent Synthetic Biology Center of Global Frontier Project (2011-0031955) funded by the Ministry of Science, ICT and Future Planning. PSD, RH, and RH were supported by the British Mycological Society and the Biotechnology and Biological Sciences Research Council (UK). ES and AAB were supported by CRC 1127 ChemBioSys and CRC-Transregio FungiNet by Deutsche Forschungsgemeinschaft (DFG). JCF was supported by Agilent Technologies (Agilent Thought Leader Award #2871) and the Novo Nordisk Foundation (Grant NNF 13OC0005201). LK was supported by the Hungarian Scientific Research Fund (NN116519) and a Bólyai János Research Fellowship. The sugar transporter analysis was supported by grants AGL2011-29925 and AGL2015-66131- AGL2015-66131-C2-2-R (MINECO/FEDER). BRO was supported by the Irving S. Johnson fund of the Kansas University endowment. We are grateful to FAPESP (The State of São Paulo Research Foundation) for the financial support (2014/06923-6 to FMS; 2012/20549-4 to ARLD; 2011/08945-9 and 2014/11766-7 to JVCO; 2012/19040-0 and 2014/10351-8 to CAU). We are grateful to the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) and Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) for the financial support (310186/2014-5 and 442333/2014-5 to FMS; 441912/2014-1 to ARLD). We acknowledge the financial support of the Dirección General de Apoyo al Personal Académico, UNAM, projects IN 225710 and IN219813, and The Slovenian Research Agency (P1-0207, P1-0391, and J4-7162). KS was supported by the Slovenian Research Agency (P1-0207) and KS and NK were supported by the Slovenian Research Agency (J4-7162). TCV and MRA acknowledge support from the Villium Foundation, Project VKR023437. GB was supported by a grant from the Deutsche Forschungsgemeinschaft (BR1502/11-2). GB and RF were supported by a grant from the Deutsche Forschungsgemeinschaft (FOR1334/2). AL was supported by St. Petersburg State University, St. Petersburg, Russia (grant no. 15.61.951.2015). The Authors thank A Gazdag, R Mohácsi, and LG Tóth (University of Debrecen) for contributing to the experimental work; and V Szabó and T Koszó (University of Debrecen) for the literature search during the construction of FSD and FSRD, respectively. The authors thank C Toft for her help in conducting the phylogenetic analysis of the sugar transporters. The authors thank DG Panaccione for providing the A. fumigatus easC mutant strain prior to publication and DR Nelson for naming CYP51 and CYP53 family representatives according to CYP nomenclature. The authors thank Arle Kruckeberg (yeast strain KY73; plasmid pYEX-BX), Barbara Bakker (yeast strain EB.VW4000), Remi Lemoine (yeast strain MaDH4), Jeremy Thorner (yeast strain SEY6210), and Ian Dawes (CMY1050) for kindly providing material used in this study Ver menos

Abstract: 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. 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. 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 Ver menos