ArticleGenome research2007
Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 99 citations in OpenAlex.
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- The mitogenomes of two saprophytic Boletales species (Computational and structural biotechnology journal · 2021Article
- Evolutionary Insights Into Two Widespread Ectomycorrhizal Fungi (Frontiers in microbiology · 2021Article
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- Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi.Molecular ecology · 2019Article
- Identification of candidate pathogenicity determinants of Rhizoctonia solani AG1-IA, which causes sheath blight disease in rice.Current genetics · 2018Article
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- Evolutionary Analysis of Pectin Lyases of the Genus Colletotrichum.Journal of molecular evolution · 2017Article
- A plant pathology perspective of fungal genome sequencing.IMA fungus · 2017Article
- Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts.Scientific reports · 2015Article
- Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens.BMC genomics · 2015Article
- The evolution of fungal metabolic pathways.PLoS genetics · 2014Article
- Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum.BMC genomics · 2014Article
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Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.