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A higher-level phylogenetic classification of the Fungi.
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Phylogenetic classification of Cordyceps and the clavicipitaceous fungi
TLDR
Most diagnostic characters used in current classifications of Cordyceps were not supported as being phylogenetically informative; the characters that were most consistent with the phylogeny were texture, pigmentation and morphology of stromata.
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Reconstructing the early evolution of Fungi using a six-gene phylogeny
TLDR
It is indicated that there may have been at least four independent losses of the flagellum in the kingdom Fungi, and the enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.
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The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
TLDR
Comparative analyses of 31 fungal genomes suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species.
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A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data
TLDR
It is demonstrated that zygomycetes comprise two major clades that form a paraphyletic grade, and the phyla Mucoromycota and ZoopagomyCota are circumscribed.
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The Fungi
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Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
TLDR
The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations.
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Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana
TLDR
Evidence is provided that genes encoding miRNAs in plants originated by inverted duplication of target gene sequences, and a model for miRNA evolution is proposed that suggests a mechanism for de novo generation of new miRNA genes with unique target specificities.
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The genome of Eucalyptus grandis
TLDR
Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes, which shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils.
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Comparative Functional Genomics of the Fission Yeasts
TLDR
Differences in gene content and regulation explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source and provide tools for investigation across the Schizosaccharomyces clade.
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