The American Academy of Microbiology has released a report (PDF) on the Fungal Kingdom outlining importance of research in the kingdom and recommending several areas of priority for future areas of research.
AAM Releases “The Fungal Kingdom” Report
Posted on July 9th, 2008 by Jason Stajich · 2 Comments
Categories: news · science policy
Tags: American Society for Microbiology, annotation, ASM, database, functional, fungal, genomes, news, reporting, reports, research, sequencing
Penicillium marneffei project
Posted on June 3rd, 2008 by Jason Stajich · 4 Comments
We’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
Categories: aspergillus · euriotiomycetes · news
Tags: comparative, comparative genomics, functional, functional genomics, funding, fungus, pathogens, penicillium
Deconstructing aflatoxin biosynthesis
Posted on April 27th, 2008 by Jason Stajich · No Comments
A paper in Science from Jason Crawford and colleagues explores the function of polyketide synthetases (PKS) in the synthesis of the secondary metabolite and carcinogen aflatoxin. Previous work (nicely reviewed in the fungi by Nancy Keller and colleagues) has shown the the PKS genes have several domains. These domains include acyl carrier protein (ACP), transacylase (SAT), ketosynthase (KS), malonyl-CoA:ACP transacylase (MAT), “product template” PT, Aand thioesterase/Claisen cyclase (TE/CLC).
Categories: PKS · aflatoxin · aspergillus
Tags: aflatoxin, aspergillus, biosynthesis, carcinogen, chemistry, enzymes, functional, fungal, fungi, pathogen, PKS, secondary metabolite
B. dendrobatidis strain JAM81 released
Posted on March 6th, 2008 by Jason Stajich · No Comments
The following is an announcement to the B.dendrobatidis and fungal community at large from Alan Kuo at JGI. This is the JAM81 strain (Jess Morgan collected from a frog in the California Sierra Nevada). The JEL423 (Joyce Longcore, collected in Panama) strain genome sequence and annotation is available from the Broad Institute.
Categories: chytridomycota · genome · news
Tags: functional, gene, genes, genome, intron, JGI, methods, news, sequencing, transcription
Some links
Posted on March 3rd, 2008 by Jason Stajich · 2 Comments
I’ve been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.
Categories: basidiomycota · database · extremophiles · molecular evolution · pathogens · zygomycete
Tags: ancestor, ancestral, brown rot, comparative, cryptococcus, database, enzymes, evolution, extremophiles, functional, fungi, fungus, genome, lignin, news, oxidoreductases, phylogenetics, reconstruction, rhizopus, taxa, toxin, white rot, yeast
Yes, Ecology can improve Genomics
Posted on October 5th, 2007 by sharpton · 1 Comment
Few organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise.
Categories: bioinformatics · comparative · functional · gene function · gene knockout · genome · genome annotation · genome sequencing · molecular evolution · saccharomyces · yeast
Tags: bioinformatics, comparative, functional, gene function, gene knockout, genome, genome annotation, genome sequencing, molecular evolution, saccharomyces, yeast
Gene knockouts in Candida parapsilosis
Posted on September 18th, 2007 by Jason Stajich · 1 Comment
A 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.
Categories: candida · functional · gene function · gene knockout · human pathogen · pathogens
Tags: candida, functional, gene function, gene knockout, human pathogen, pathogens
That was a lot of work
Posted on April 3rd, 2007 by sharpton · No Comments
I’ve never worked with Magnaporthe grisea, the fungus responsible for rice blast, one of the most devastating crop diseases, but I do know that its life cycle is complicated and that knocking out roughly 61% of the genes in the genome and evaluating the mutant phenotype to infer gene function is not trivial. In their recent letter to Nature, Jeon et al did what many
Categories: functional · fungi · gene function · genome · genome annotation · magnaporthe · plant pathogen
Tags: functional, fungi, gene function, genome, genome annotation, magnaporthe, plant pathogen
Approaching 100% coverage for GO assignments in S.pombe
Posted on March 4th, 2007 by Jason Stajich · 2 Comments
A paper by Martin Aslett and Val Wood indicate that the fission yeast community is approaching 100% coverage of a GO annotation for every gene in the S. pombe genome. Only Ashbya gossypii has a smaller genome in the fungi (see a recent paper
Categories: functional · genome annotation · s.pombe
Tags: annotation database, dataset, fission yeast, functional, fungi, genes, genome annotation, japonicus, pombe, yeast community
Making the Revolution Work for You
Posted on January 30th, 2007 by sharpton · No Comments
In a recent Microbiology Mini-Review, Meriel Jones catalogs both the potential benefits and problems that arise from fungal genome sequencing.
Categories: aspergillus · comparative · database · functional · fungi · genome
Tags: aspergillus, comparative, database, functional, fungi, genome
