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Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
TLDR
The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described. Expand
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. Expand
The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.
TLDR
A 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi, and a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions support a terrestrial, saprobic ecology as ancestral are presented. Expand
A class-wide phylogenetic assessment of Dothideomycetes
TLDR
A genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon. Expand
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)
TLDR
This work assembled 89 scaffolds to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models, providing a roadmap for constructing enhanced T.Reesei strains for industrial applications such as biofuel production. Expand
A phylogenomic analysis of the Ascomycota.
TLDR
An automated procedure was developed to extract orthologous sequences from fungal genomes and incorporate them into phylogenomic analyses in a timely and efficient manner, demonstrating the correct identification of orthologs and the ability to incorporate unannotated genomic data into a common phylogenetic analysis. Expand
Functional Analysis of All Nonribosomal Peptide Synthetases in Cochliobolus heterostrophus Reveals a Factor, NPS6, Involved in Virulence and Resistance to Oxidative Stress
TLDR
Only NPS 6 is unfailingly conserved among euascomycete fungi, suggesting the possibility that NPS6 activity provides oxidative stress protection during both saprobic and parasitic growth. Expand
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina).
TLDR
This work assembled 89 scaffolds to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models, providing a roadmap for constructing enhanced T.Reesei strains for industrial applications such as biofuel production. Expand
International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi.
TLDR
An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool to rapidly and reliably identify most agents of mycoses. Expand
Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence
TLDR
Comparison of the genomes of three P. tritici-repentis isolates provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes. Expand
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