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The generic genome browser: a building block for a model organism system database.
TLDR
The Generic Genome Browser (GBrowse) is described, a Web-based application for displaying genomic annotations and other features and easy integration with other components of a model organism system Web site.
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The Bioperl toolkit: Perl modules for the life sciences.
TLDR
The overall architecture of the Bioperl toolkit is described, the problem domains that it addresses, and specific examples of how the toolkit can be used to solve common life-sciences problems are given.
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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.
View on Nature
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
TLDR
Comparisons of the two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers, which will help to understand the evolutionary forces that mold nematode genomes.
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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.
View on Taylor & Francis
The Fungi
View on Elsevier
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis
TLDR
The discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate previously unknown mechanisms of pathogenicity operating in biotrophic fungi.
View on Nature
Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak
TLDR
It is demonstrated how cryptic same-sex reproduction can enable expansion of a human pathogen to a new geographical niche and contribute to the ongoing production of infectious spores.
View on Nature
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
TLDR
The predicted gene inventory of the L. bicolor genome points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi, providing an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
View on Nature
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
TLDR
This work has constructed robust phylogenies for fungi based on whole genome analysis that provide strong support for the classification of phyla, sub-phyla, classes and orders.
View on Springer
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