Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi

Abstract

The recent proliferation of genome sequencing in diverse fungal species has provided the first opportunity for comparative genome analysis across a eukaryotic kingdom. Here, we report a comparative study of 34 complete fungal genome sequences, representing a broad diversity of Ascomycete, Basidiomycete, and Zygomycete species. We have clustered all predicted protein-encoding gene sequences from these species to provide a means of investigating gene innovations, gene family expansions, protein family diversification, and the conservation of essential gene functions-empirically determined in Saccharomyces cerevisiae-among the fungi. The results are presented with reference to a phylogeny of the 34 fungal species, based on 29 universally conserved protein-encoding gene sequences. We contrast this phylogeny with one based on gene presence and absence and show that, while the two phylogenies are largely in agreement, there are differences in the positioning of some species. We have investigated levels of gene duplication and demonstrate that this varies greatly between fungal species, although there are instances of coduplication in distantly related fungi. We have also investigated the extent of orthology for protein families and demonstrate unexpectedly high levels of diversity among genes involved in lipid metabolism. These analyses have been collated in the e-Fungi data warehouse, providing an online resource for comparative genomic analysis of the fungi.

Defects in Mitochondrial and Peroxisomal β-Oxidation Influence Virulence in the Maize Pathogen Ustilago maydis

“…Similar results were obtained with a scdA echA double mutant in Podospora anserina (4). Recent in silico surveys of the pathways encoded in more than 50 fungal genomes revealed that most fungi possess both mitochondrial and peroxisomal pathways (8,52).…”

Peroxisomal and Mitochondrial β-Oxidation Pathways Influence the Virulence of the Pathogenic Fungus Cryptococcus neoformans

“…Fungal ␤-oxidation is not well characterized, and it was previously thought that fungi might have peroxisomal ␤-oxidation only because Saccharomyces cerevisiae lacks the enzymes for mitochondrial ␤-oxidation (73,75). However, recent in silico surveys of the pathways encoded in more than 50 fungal genomes revealed that most fungi possess both mitochondrial and peroxisomal pathways (10,69). Mitochondrial ␤-oxidation has also been convincingly demonstrated in the saprophytic ascomycete Aspergillus nidulans (26,44,45).…”

Fungal physiology – a future perspective

“…The comparison of annotated genomes from many related species can highlight common core components of these signalling cascades, while global analyses of changes in gene expression under different environmental conditions and developmental stages can be used to identify downstream targets. However, comparative genomic studies of fungi are currently somewhat limited, due to the relative paucity of well-annotated fungal genomes and the large proportion of genes in fungi with no known function (Cornell et al, 2007;Soanes et al, 2007). Benefiting from advances in next-generation sequencing, this situation is likely to change with the routine use of affordable, massively parallel sequencing platforms such as the 454 from Roche, the Applied Biosystems SOLiD and the Illumina GA2.…”