The Hyphal Tip

Digesting the fungal genomes

The Hyphal Tip header image 4

A word about databases

Posted on July 27th, 2008 by Jason Stajich · 1 Comment

Logo for fungal GenomesReport concludes that a fungal genome database is of “the highest priority”.

This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom.

[Read more →]

Categories: opinion
Tags: , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,

Cochliobolus genome released

Posted on July 17th, 2008 by Jason Stajich · 1 Comment

Just noticed that the [[JGI]] has released the Cochliobolus heterostrophus genome sequence at their site predicting 9,633 protein-coding genes.  Torrey Mesa Research Institute had access to a sequence many years ago, but it isn’t until now that public version of this genome is available.  Cochliobolus is has been a model plant pathogen system and its production of T-Toxin by a PKS gene (Yang et al)

[Read more →]

Categories: pezizomycota
Tags: , , , , , , , , ,

Penicillium marneffei project

Posted on June 3rd, 2008 by Jason Stajich · 4 Comments

P.marneffeiWe’re excited that a Penicillium marneffei grant to Mat Fisher and collaborators has been funded by the Welcome Trust. It includes a collaboration with University College London, our lab, JCVI, and Univ of Melbourne. This project will explore functional and comparative genomics approaches to studying the fungus

[Read more →]

Categories: aspergillus · euriotiomycetes · news
Tags: , , , , , , ,

Trichoderma reesei genome paper published

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

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.

[Read more →]

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

More RIP without sex?

Posted on April 5th, 2008 by Jason Stajich · 1 Comment

Another asexual species of fungi also has evidence for the meiosis-specific process of Repeat Induced Point-mutations (RIP).

[Read more →]

Categories: RIP · neurospora · pezizomycota · sordariomycetes
Tags: , , , , , , , , , , , , , , , , , , , , , ,

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

[Read more →]

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

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.

[Read more →]

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

Candida White-Opaque switching

Posted on October 31st, 2007 by Jason Stajich · No Comments

Blogging on Peer-Reviewed ResearchA paper in PLoS Biology from Sandy Johnson’s lab entitled “Interlocking Transcriptional Feedback Loops Control White-Opaque Switching in Candida albicans” discusses phenotype switching in the human pathogenic fungus Candida albicans. Why is the important?

[Read more →]

Categories: candida · development · human pathogen
Tags: , , , , , , , , , , , ,

Exploring CUG codon evolution in Candida

Posted on October 9th, 2007 by Jason Stajich · 1 Comment

Reverting CUG tRNA from derived change coding for serine back to leucine (standard code) has profound effect on organism.

[Read more →]

Categories: candida · evolution · fungi · gene regulation · genetic code
Tags: , , , , , , , , , , , ,

Gene knockouts in Candida parapsilosis

Posted on September 18th, 2007 by Jason Stajich · 1 Comment

Cparapsilosis from G.ButlerA recent paper “Targeted gene deletion in Candida parapsilosis demonstrates the role of secreted lipase in virulence”, from the Nosanchuk lab at Yeshiva University, shows the role of secreted lipases in virulence of this pathogen.

[Read more →]

Categories: candida · functional · gene function · gene knockout · human pathogen · pathogens
Tags: , , , , ,