Genomic Diversity in the Genus of Aspergillus

Research output: Book/ReportPh.D. thesis


Aspergillus is a highly important genus of saprotrophic filamentous fungi. It is a very diverse genus that is inextricably intertwined with human a↵airs on a daily basis, holding species relevant to plant and human pathology, enzyme and bulk chemistry production, food and beverage biotechnology, and scientific model organisms. The phenotypic diversity in this genus is extraordinary and identifying the genetic basis for this diversity has great potential for academia and industry. When the genomic era began for Aspergillus in 2005 with the genome sequences of A. nidulans, A. oryzae and A. fumigatus, it was quickly apparent that a large part of understanding the individual species and genetic features comes from preforming comparative genomics. This is what the Aspergillus whole-genus sequencing project will facilitate, which aim to sequence and study the genomes of all 350 members in genus Aspergillus. This thesis has utilized this resource to study the genome diversity in the Aspergillus genus, with a focus on how the genetic variation a↵ects speciation. In the work presented here, a new homolog identification tool has been developed based on BLAST alignments of protein sequences and single linkage. The advantage of this tool is its ability to link homologs with diverse evolutionary histories, thus accommodating the genetic variances that has accumulated over > 200 million years in genus Aspergillus. Throughout this work, HomologSL has been used to investigate genome diversity within species, clades, sections and genus of Aspergillus. The work uncovers a large genomic diversity across all studied groups of species. The genomic diversity was especially evident on the section level, where the proteins shared by all species only represents ⇠55% of the proteome. This number decreases even further, to 38%, for protein shared by the whole genus. The work further identifies the species-unique genes holding a large unexplored potential of both enzymes and secondary metabolites. Through the analysis of the shared and species-unique genes, this study presents genes and functions that defines genus Aspergillus, sections Nigri, Usti and Cavericolus, clade Tubingensis, and species A. niger. It lastly uses these results to predict genetic traits that take part in fungal speciation. Within a few years the Aspergillus whole-genus sequencing project will have published all currently-accepted Aspergillus genomes, providing the Aspergillus community with a resource that will allow for research within comparative genomics, which has not been possible in any fungal genera before. The work presented here is part of this project, releasing both comparative genomics tools and > 40 genomes to make it happen.
Original languageEnglish
PublisherTechnical University of Denmark
Number of pages9
Publication statusPublished - 2017

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PhD Thesis - is currently confidential, will be updated later.

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