학술논문

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
Document Type
article
Author
de Vries, Ronald PRiley, RobertWiebenga, AdAguilar-Osorio, GuillermoAmillis, SotirisUchima, Cristiane AkemiAnderluh, GregorAsadollahi, MojtabaAskin, MarionBarry, KerrieBattaglia, EvyBayram, ÖzgürBenocci, TizianoBraus-Stromeyer, Susanna ACaldana, CamilaCánovas, DavidCerqueira, Gustavo CChen, FushengChen, WanpingChoi, CindyClum, Aliciados Santos, Renato Augusto CorrêaDamásio, André Ricardo de LimaDiallinas, GeorgeEmri, TamásFekete, ErzsébetFlipphi, MichelFreyberg, SusanneGallo, AntoniaGournas, ChristosHabgood, RobHainaut, MatthieuHarispe, María LauraHenrissat, BernardHildén, Kristiina SHope, RyanHossain, AbeerKarabika, EugeniaKaraffa, LeventeKarányi, ZsoltKraševec, NadaKuo, AlanKusch, HaraldLaButti, KurtLagendijk, Ellen LLapidus, AllaLevasseur, AnthonyLindquist, ErikaLipzen, AnnaLogrieco, Antonio FMacCabe, AndrewMäkelä, Miia RMalavazi, IranMelin, PetterMeyer, VeraMielnichuk, NataliaMiskei, MártonMolnár, Ákos PMulé, GiuseppinaNgan, Chew YeeOrejas, MargaritaOrosz, ErzsébetOuedraogo, Jean PaulOverkamp, Karin MPark, Hee-SooPerrone, GiancarloPiumi, FrancoisPunt, Peter JRam, Arthur FJRamón, AnaRauscher, StefanRecord, EricRiaño-Pachón, Diego MauricioRobert, VincentRöhrig, JulianRuller, RobertoSalamov, AsafSalih, Nadhira SSamson, Rob ASándor, ErzsébetSanguinetti, ManuelSchütze, TabeaSepčić, KristinaShelest, EkaterinaSherlock, GavinSophianopoulou, VickySquina, Fabio MSun, HuiSusca, AntoniaTodd, Richard BTsang, AdrianUnkles, Shiela Evan de Wiele, Nathalievan Rossen-Uffink, DianaOliveira, Juliana Velasco de CastroVesth, Tammi CVisser, JaapYu, Jae-HyukZhou, MiaomiaoAndersen, Mikael R
Source
Genome Biology. 18(1)
Subject
Human Genome
Genetics
Biotechnology
Emerging Infectious Diseases
Infectious Diseases
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
Genome sequencing
Comparative genomics
Fungal biology
Environmental Sciences
Biological Sciences
Information and Computing Sciences
Bioinformatics
Language
Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsMany 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.