The [[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.
Trichoderma reesei genome paper published
Posted on May 12th, 2008 by Jason Stajich · 1 Comment
Categories: filamentous · gene family · genome · genome annotation · genome sequencing · trichoderma
Tags: aspergillus, biofuel, cellulase, comparative, database, definitions, enzymes, evolution, fermentation, filamentous, fungi, fungus, fusarium, genome, genomes, JGI, magnaporthe, pathogens, phylogenetics, s, sequences, sequencing, species, systematics, trichoderma
(re)Annotating GenBank
Posted on March 22nd, 2008 by Jason Stajich · No Comments
Tom Bruns, Martin Bidartondo and 250 others sent a letter to Science describing the current problems with fixing annotation in GenBank. There is an entertaining accompanying news article that interviews several people about the problem of updating annotation and species assigned to sequences in the database. In particular the problem for mycologists that many fungi found from metagenomic approaches are only identified through molecular sequences and having the wrong species associated with a sequence can be difficult when studying community ecology composition. This problem is not limited to fungi by any means, but recent reports find as many as 20% of fungal Intergenic Spacer (ITS) sequences are mis-attributed to the wrong species.
There’s a nice quote in the news article from Steven Salzberg talking about the difficulties in getting sequences, especially from big centers, updated. I’m sure he is thinking of many examples, like reclassifying some Drosophila sequence traces.
Categories: database · fungi · metagenomics · news
Tags: alignment, database, definitions, experimental, fungi, gene, genes, genome, metagenomics, news, phylogenetics, sequencing, wiki
Cryptococcus species deliniation
Posted on February 17th, 2008 by Jason Stajich · No Comments
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
Categories: cryptococcus · human pathogen · phylogenetics · phylogeny · speciation
Tags: cryptococcus, definitions, filamentous, fungi, fungus, genome, neurospora, pathogen, pathogens, phylogenetics, sequencing
Defining “gene”
Posted on November 29th, 2007 by Jason Stajich · 1 Comment
The term “gene” might be tired and perhaps because it can have many different meanings – (don’t get us started on homolog!). We of course know that one gene/one enzyme hypothesis and the central dogma fails to represent full complexity of the RNA world, pre- and post-transcriptional gene regulation, and post-transcriptional modifications. An [...]
Categories: defintions
Tags: definitions, dene, gene, philosophy
Fungal Genetics 2007 details
Posted on March 28th, 2007 by Jason Stajich · 2 Comments
I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.
If there was any theme in the conference it was “Hey we are all using these genome sequences”.
Categories: Fungal Genetics · bioinformatics · chytridomycota · cryptococcus · dothideomycetes · euriotiomycetes · filamentous · glomeromycota · homobasidiomycota · horizontal gene transfer · neurospora · news · sordariomycetes · zygomycete
Tags: annotation, annotations, asilomar, aspergillus, basidiomycete, batrachochytrium, bioinforics, biology, candida, chytrid, clone, comparative, conferences & courses, coprinus, cryptococcus, definitions, development, diversity, ecology, endophyte, enzymes, evolution, experimental, frog, fungal, fungi, fungus, gene, genes, genome, genomes, horizontaltransfer, infection, JGI, maps, MAT, meetings, methods, microarray, microbes, multicellularity, mycological, neurospora, news, NRPS, organisms, pathogen, pathogens, phenotype, philosophy, phylogenetics, plant, plants, podospora, pombe, protein, repeats, rhizopus, RIP, s, saccharomyces, seminar, sequences, sequencing, SOLiD, speciation, species, strain, taxa, transcription, transcripts, wheat, yeast, zygomycete, zygomycetes
