@article{3058603,
    title = "Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus",
    author = "de Vries, R.P. and Riley, R. and Wiebenga, A. and Aguilar-Osorio, G. and Amillis, S. and Uchima, C.A. and Anderluh, G. and Asadollahi, M. and Askin, M. and Barry, K. and Battaglia, E. and Bayram, O. and Benocci, T. and Braus-Stromeyer, S.A. and Caldana, C. and Cánovas, D. and Cerqueira, G.C. and Chen, F. and Chen, W. and Choi, C. and Clum, A. and dos Santos, R.A.C. and de Lima Damásio, A.R. and Diallinas, G. and Emri, T. and Fekete, E. and Flipphi, M. and Freyberg, S. and Gallo, A. and Gournas, C. and Habgood, R. and Hainaut, M. and Harispe, M.L. and Henrissat, B. and Hildén, K.S. and Hope, R. and Hossain, A. and Karabika, E. and Karaffa, L. and Karányi, Z. and Kraševec, N. and Kuo, A. and Kusch, H. and LaButti, K. and Lagendijk, E.L. and Lapidus, A. and Levasseur, A. and Lindquist, E. and Lipzen, A. and Logrieco, A.F. and MacCabe, A. and Mäkelä, M.R. and Malavazi, I. and Melin, P. and Meyer, V. and Mielnichuk, N. and Miskei, M. and Molnár, A.P. and Mulé, G. and Ngan, C.Y. and Orejas, M. and Orosz, E. and Ouedraogo, J.P. and Overkamp, K.M. and Park, H.-S. and Perrone, G. and Piumi, F. and Punt, P.J. and Ram, A.F.J. and Ramón, A. and Rauscher, S. and Record, E. and Riaño-Pachón, D.M. and Robert, V. and Röhrig, J. and Ruller, R. and Salamov, A. and Salih, N.S. and Samson, R.A. and Sándor, E. and Sanguinetti, M. and Schütze, T. and Sepčić, K. and Shelest, E. and Sherlock, G. and Sophianopoulou, V. and Squina, F.M. and Sun, H. and Susca, A. and Todd, R.B. and Tsang, A. and Unkles, S.E. and van de Wiele, N. and van Rossen-Uffink, D. and de Castro Oliveira, J.V. and Vesth, T.C. and Visser, J. and Yu, J.-H. and Zhou, M. and Andersen, M.R. and Archer, D.B. and Baker, S.E. and Benoit, I. and Brakhage, A.A. and Braus, G.H. and Fischer, R. and Frisvad, J.C. and Goldman, G.H. and Houbraken, J. and Oakley, B. and Pócsi, I. and Scazzocchio, C. and Seiboth, B. and vanKuyk, P.A. and Wortman, J. and Dyer, P.S. and Grigoriev, I.V.",
    journal = "Genome Biology",
    year = "2017",
    volume = "18",
    number = "1",
    publisher = "BioMed Central Ltd.",
    issn = "1465-6906, 1474-760X",
    doi = "10.1186/s13059-017-1151-0",
    keywords = "Article;  asexual reproduction;  Aspergillus;  controlled study;  fungal gene;  fungal genome;  fungal reproduction;  fungus identification;  gene function;  gene identification;  genome analysis;  genome-wide association study;  molecular phylogeny;  nonhuman;  secondary metabolism;  sequence analysis;  species diversity;  adaptation;  Aspergillus;  biodiversity;  biology;  biomass;  classification;  DNA methylation;  gene expression regulation;  gene regulatory network;  genetics;  genomics;  human;  metabolism;  microbiology;  molecular genetics;  multigene family;  phylogeny;  physiological stress;  plant;  procedures;  signal transduction, carbon;  cytochrome P450;  fungal protein;  oxidoreductase, Adaptation, Biological;  Aspergillus;  Biodiversity;  Biomass;  Carbon;  Computational Biology;  Cytochrome P-450 Enzyme System;  DNA Methylation;  Fungal Proteins;  Gene Expression Regulation, Fungal;  Gene Regulatory Networks;  Genome, Fungal;  Genomics;  Humans;  Metabolic Networks and Pathways;  Molecular Sequence Annotation;  Multigene Family;  Oxidoreductases;  Phylogeny;  Plants;  Secondary Metabolism;  Signal Transduction;  Stress, Physiological",
    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. © 2017 The Author(s)."
}