Dataset Information

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

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.

SUBMITTER: de Vries RP

PROVIDER: S-EPMC5307856 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

de Vries Ronald P RP Riley Robert R Wiebenga Ad A Aguilar-Osorio Guillermo G Amillis Sotiris S Uchima Cristiane Akemi CA Anderluh Gregor G Asadollahi Mojtaba M Askin Marion M Barry Kerrie K Battaglia Evy E Bayram Özgür Ö Benocci Tiziano T Braus-Stromeyer Susanna A SA Caldana Camila C Cánovas David D Cerqueira Gustavo C GC Chen Fusheng F Chen Wanping W Choi Cindy C Clum Alicia A Dos Santos Renato Augusto Corrêa RA Damásio André Ricardo de Lima AR Diallinas George G Emri Tamás T Fekete Erzsébet E Flipphi Michel M Freyberg Susanne S Gallo Antonia A Gournas Christos C Habgood Rob R Hainaut Matthieu M Harispe María Laura ML Henrissat Bernard B Hildén Kristiina S KS Hope Ryan R Hossain Abeer A Karabika Eugenia E Karaffa Levente L Karányi Zsolt Z Kraševec Nada N Kuo Alan A Kusch Harald H LaButti Kurt K Lagendijk Ellen L EL Lapidus Alla A Levasseur Anthony A Lindquist Erika E Lipzen Anna A Logrieco Antonio F AF MacCabe Andrew A Mäkelä Miia R MR Malavazi Iran I Melin Petter P Meyer Vera V Mielnichuk Natalia N Miskei Márton M Molnár Ákos P ÁP Mulé Giuseppina G Ngan Chew Yee CY Orejas Margarita M Orosz Erzsébet E Ouedraogo Jean Paul JP Overkamp Karin M KM Park Hee-Soo HS Perrone Giancarlo G Piumi Francois F Punt Peter J PJ Ram Arthur F J AF Ramón Ana A Rauscher Stefan S Record Eric E Riaño-Pachón Diego Mauricio DM Robert Vincent V Röhrig Julian J Ruller Roberto R Salamov Asaf A Salih Nadhira S NS Samson Rob A RA Sándor Erzsébet E Sanguinetti Manuel M Schütze Tabea T Sepčić Kristina K Shelest Ekaterina E Sherlock Gavin G Sophianopoulou Vicky V Squina Fabio M FM Sun Hui H Susca Antonia A Todd Richard B RB Tsang Adrian A Unkles Shiela E SE van de Wiele Nathalie N van Rossen-Uffink Diana D Oliveira Juliana Velasco de Castro JV Vesth Tammi C TC Visser Jaap J Yu Jae-Hyuk JH Zhou Miaomiao M Andersen Mikael R MR Archer David B DB Baker Scott E SE Benoit Isabelle I Brakhage Axel A AA Braus Gerhard H GH Fischer Reinhard R Frisvad Jens C JC Goldman Gustavo H GH Houbraken Jos J Oakley Berl B Pócsi István I Scazzocchio Claudio C Seiboth Bernhard B vanKuyk Patricia A PA Wortman Jennifer J Dyer Paul S PS Grigoriev Igor V IV

Genome biology 20170214 1

<h4>Background</h4>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.<h4>Results</h4>We have generated genome se ...[more]

PMID: 28196534

Similar Datasets

Project description:BackgroundGenetic variation in the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has been studied among fungi. However, the numbers of ITS sequence polymorphisms in the various Candida species and their associations with sources of invasive fungal infections remain poorly investigated. Here, we characterized the intraspecific and interspecific ITS diversity of Candida spp. strains collected from patients with bloodstream or oroesophageal candidiasis.MethodsWe selected cultures of representative medically important species of Candida as well as some rare and emerging pathogens. Identification was performed by micromorphology and by biochemical testing using an ID32C system, as well as by the sequencing of rDNA ITS. The presence of intraspecific ITS polymorphisms was characterized based on haplotype networks, and interspecific diversity was characterized based on Bayesian phylogenetic analysis.ResultsAmong 300 Candida strains, we identified 76 C. albicans, 14 C. dubliniensis, 40 C. tropicalis, 47 C. glabrata, 34 C. parapsilosis (sensu stricto), 31 C. orthopsilosis, 3 C. metapsilosis, 21 Meyerozyma guilliermondii (C. guilliermondii), 12 Pichia kudriavzevii (C. krusei), 6 Clavispora lusitaniae (C. lusitaniae), 3 C. intermedia, 6 Wickerhamomyces anomalus (C. pelliculosa), and 2 C. haemulonii strains, and 1 C. duobushaemulonii, 1 Kluyveromyces marxianus (C. kefyr), 1 Meyerozyma caribbica (C. fermentati), 1 Pichia norvegensis (C. norvegensis), and 1 Lodderomyces elongisporus strain. Out of a total of seven isolates with inconsistent ID32C profiles, ITS sequencing identified one C. lusitaniae strain, three C. intermedia strains, two C. haemulonii strains and one C. duobushaemulonii strain. Analysis of ITS variability revealed a greater number of haplotypes among C. albicans, C. tropicalis, C. glabrata and C. lusitaniae, which are predominantly related to endogenous sources of acquisition. Bayesian analysis confirmed the major phylogenetic relationships among the isolates and the molecular identification of the different Candida spp.ConclusionsMolecular studies based on ITS sequencing are necessary to identify closely related and emerging species. Polymorphism analysis of the ITS rDNA region demonstrated its utility as a genetic marker for species identification and phylogenetic relationships as well as for drawing inferences concerning the natural history of hematogenous infections caused by medically important and emerging Candida species.

Project description:The filamentous fungal family Aspergillaceae contains >1,000 known species, mostly in the genera Aspergillus and Penicillium Several species are used in the food, biotechnology, and drug industries (e.g., Aspergillus oryzae and Penicillium camemberti), while others are dangerous human and plant pathogens (e.g., Aspergillus fumigatus and Penicillium digitatum). To infer a robust phylogeny and pinpoint poorly resolved branches and their likely underlying contributors, we used 81 genomes spanning the diversity of Aspergillus and Penicillium to construct a 1,668-gene data matrix. Phylogenies of the nucleotide and amino acid versions of this full data matrix as well as of several additional data matrices were generated using three different maximum likelihood schemes (i.e., gene-partitioned, unpartitioned, and coalescence) and using both site-homogenous and site-heterogeneous models (total of 64 species-level phylogenies). Examination of the topological agreement among these phylogenies and measures of internode certainty identified 11/78 (14.1%) bipartitions that were incongruent and pinpointed the likely underlying contributing factors, which included incomplete lineage sorting, hidden paralogy, hybridization or introgression, and reconstruction artifacts associated with poor taxon sampling. Relaxed molecular clock analyses suggest that Aspergillaceae likely originated in the lower Cretaceous and that the Aspergillus and Penicillium genera originated in the upper Cretaceous. Our results shed light on the ongoing debate on Aspergillus systematics and taxonomy and provide a robust evolutionary and temporal framework for comparative genomic analyses in Aspergillaceae More broadly, our approach provides a general template for phylogenomic identification of resolved and contentious branches in densely genome-sequenced lineages across the tree of life.IMPORTANCE Understanding the evolution of traits across technologically and medically significant fungi requires a robust phylogeny. Even though species in the Aspergillus and Penicillium genera (family Aspergillaceae, class Eurotiomycetes) are some of the most significant technologically and medically relevant fungi, we still lack a genome-scale phylogeny of the lineage or knowledge of the parts of the phylogeny that exhibit conflict among analyses. Here, we used a phylogenomic approach to infer evolutionary relationships among 81 genomes that span the diversity of Aspergillus and Penicillium species, to identify conflicts in the phylogeny, and to determine the likely underlying factors of the observed conflicts. Using a data matrix comprised of 1,668 genes, we found that while most branches of the phylogeny of the Aspergillaceae are robustly supported and recovered irrespective of method of analysis, a few exhibit various degrees of conflict among our analyses. Further examination of the observed conflict revealed that it largely stems from incomplete lineage sorting and hybridization or introgression. Our analyses provide a robust and comprehensive evolutionary genomic roadmap for this important lineage, which will facilitate the examination of the diverse technologically and medically relevant traits of these fungi in an evolutionary context.

Dataset Information

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

Background

Results

Conclusions

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets