The Hyphal Tip: Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

The Hyphal Tip: Fungal Genomes and Comparative Genomics header image 4

Trichoderma reesei genome paper published

Posted on May 12th, 2008 by Jason Stajich · No Comments

TrichodermaThe [[Trichoderma reesei]] genome paper was recently published in Nature Biotechnology from Diego Martinez at [[LANL]] with collaborators at [[JGI]], [[LBNL]], and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol production.

Click to continue reading "Trichoderma reesei genome paper published"

[Read more →]

Categories: filamentous · gene family · genome · genome annotation · genome sequencing · trichoderma

Podospora genome published

Posted on May 11th, 2008 by Jason Stajich · No Comments

P.anserinaThe genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings.  The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons
Click to continue reading "Podospora genome published"

[Read more →]

Categories: comparative · genome · genome sequencing · neurospora · sordariomycetes

Aspergillus comparative transcriptional profiling

Posted on March 12th, 2008 by Jason Stajich · 1 Comment

ResearchBlogging.org

Researchers from Technical University of Denmark published some interesting results from comparing expression across the very distinct Aspergillus species.

Kudos also goes to making it Open Access. I am posting a few key figures below the fold because I can! They grew the fungi in bioreactors fermenting glucose or xylose. After calibrating the growth curves they were able to sample the appropriate time points for comparison of gene expression across these three species. They found a set of genes commonly expressed.

Click to continue reading "Aspergillus comparative transcriptional profiling"

[Read more →]

Categories: aspergillus · evolution · gene regulation · microarray

Cryptococcus species deliniation

Posted on February 17th, 2008 by Jason Stajich · No Comments

ResearchBlogging.org What delineates species boundaries in fungi? Much work has been done on biological and phylogenetic species concepts in fungi. Some concepts are reviewed in Taylor et al 2006 and in Taylor et al 2000, and applications can be seen in several pathogens such as Paraccocidiodies, Coccidioides, and the model filamentous (non-pathogenic) fungus Neurospora

Click to continue reading "Cryptococcus species deliniation"

[Read more →]

Categories: cryptococcus · human pathogen · phylogenetics · phylogeny · speciation

Phytopathogenic Fungi: what have we learned from genome sequences?

Posted on February 8th, 2008 by Jason Stajich · No Comments

ResearchBlogging.orgA review in Plant Cell from Darren Soanes and colleagues summarizes some of the major findings about evolution of phytopathogenic fungi gleaned from genome sequencing highlighting 12 fungi and 2 oomycetes. By mapping evolution of genes identified as virulence factors as well as genes that appear to have similar patterns of diversification, we can hope to derive some principals about how phytopathogenic fungi have evolved from saprophyte ancestors.

Click to continue reading "Phytopathogenic Fungi: what have we learned from genome sequences?"

[Read more →]

Categories: comparative · dothideomycetes · euriotiomycetes · fusarium · magnaporthe · phylogeny · plant pathogen · secondary metabolite

Neurospora speciation through experimental evolution

Posted on February 5th, 2008 by Jason Stajich · No Comments

ResearchBlogging.orgDettman, Anderson, and Kohn recently published a paper in BMC Evolutionary Biology on reproductive experimental evolution in two Neurospora crassa populations evolved under different selective conditions. This is a great study that complements work published last year in Nature on experimental evolution in Saccharomyces cerevisiae populations. Neurospora populations were evolved under high salt and low temperature and were started from either high diversity (interspecific crosses, N. crassa vs N. intermedia) or low diversity (intraspecific cross, two N. crassa isolates D143 (Louisiana, USA)and D69 (Ivory Coast)) as described in Figure 1. The experimentally evolved populations were then tested for asexual and sexual fitness (they were taken through complete meiotic cycle throughout the experiment to avoid insure there was selection on the sexual reproduction pathway.

Click to continue reading "Neurospora speciation through experimental evolution"

[Read more →]

Categories: adaptation · experimental evolution · neurospora · speciation

Fusarium graminearum genome published

Posted on September 8th, 2007 by Jason Stajich · 1 Comment

The genome of the wheat and cereal pathogen Fusarium graminearum was published in Science this week in an article entitled "The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specializationtion". The project was a collaboration of many different Fusarium research groups.
Click to continue reading "Fusarium graminearum genome published"

[Read more →]

Categories: RIP · filamentous · fusarium · genome · genome annotation · genome sequencing · plant pathogen

Evolution of PEX genes

Posted on June 7th, 2007 by Jason Stajich · 2 Comments

A nice evolutionary analysis of peroxin genes entitled PEX Genes in Fungal Genomes: Common, Rare, or Redundant in the journal "Traffic" from Kiel et al out of the University of Groningen in The Netherlands. Within a species, the genes in the PEX family are not necessarily phylogenetically related to each other, but instead are all named as to how they were discovered in mutant screens.
Click to continue reading "Evolution of PEX genes"

[Read more →]

Categories: aspergillus · cell biology · comparative · evolution · filamentous · fungi · peroxisome

More Euriotiomycete genomes

Posted on May 25th, 2007 by Jason Stajich · No Comments

P.marneffeiThe genome sampling in the Eurotiomycota clade just keeps getting better. The new J. Crag Venter Institute (TIGR) deposited WGS Assemblies of the human pathogens Penicillium marneffei and Talaromyces stipitatus. P. marneffei is a thermally dimorphic fungus endemic to South-East Asia found in bamboo rats. It is studied by a number of
Click to continue reading "More Euriotiomycete genomes"

[Read more →]

Categories: euriotiomycetes · filamentous · fungi · genome · news

Clusters of genomes

Posted on May 14th, 2007 by Jason Stajich · No Comments

As announced at the Fungal Genetics meeting, the FGI at the Broad Institute is focusing on clusters of genomes rather than single ones. Some of genome projects are already grouped.
  • Coccidioides has 3 strains already plus the outgroup Uncinocarpus and conceivable one could include Histoplasma in there. This resources will grow to 14 strains (which comprise two species) of Coccidioides contributed by FGI and
Click to continue reading "Clusters of genomes"

[Read more →]

Categories: aspergillus · cryptococcus · filamentous · fungi · fusarium · genome