Entries from March 2008
Mold farm?
Posted on March 31st, 2008 by Jason Stajich · No Comments
Of frogs and fungi
Posted on March 26th, 2008 by Jason Stajich · No Comments
Categories: chytridomycota · pathogens
RIPing in an asexual fungus
Posted on March 23rd, 2008 by Jason Stajich · 3 Comments
A paper in Current Genetics describes the discovery of Repeat Induced Polymorphism (RIP) in two Euriotiales fungi. RIP has been extensively studied in Neurospora crassa and has been identified in other Sordariomycete fungi Magnaporthe, Fusiarium. This is not the first Aspergillus species to have RIP described as it was demonstrated in the biotech workhorse Aspergillus oryzae. However, I think this study is the first to describe RIP in a putatively asexual fungus. The evidence for RIP is only found in transposon sequences in the Aspergillus and Penicillium. A really interesting aspect of this discovery is RIP is thought to only occur during sexual stage, but a sexual state has never been observed for these fungi.
Categories: RIP · aspergillus · fusarium · magnaporthe · neurospora
(re)Annotating GenBank
Posted on March 22nd, 2008 by Jason Stajich · No Comments
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
Throw away that field guide, just use echolocation
Posted on March 21st, 2008 by Jason Stajich · No Comments
Categories: fungi
Ireland's blight and Puccinia update
Posted on March 17th, 2008 by Jason Stajich · 2 Comments
Hyphoid logic points out that it is appropriate to discuss about the oomycete Phytophthora infestans on St. Patrick's Day and mentions a NYT article "The fungus that conquered Europe" that is worth a look.
It is also worth thinking about another blight, well rust, that is spreading through the middle east and could threaten wheat crops worldwide. New Scientist has excellent coverage of Puccinia
Categories: oomycete · plant pathogen · rusts
Aspergillus comparative transcriptional profiling
Posted on March 12th, 2008 by Jason Stajich · 1 Comment
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.
Categories: aspergillus · evolution · gene regulation · microarray
Fun with estimating divergence times
Posted on March 11th, 2008 by Jason Stajich · No Comments
Estimating divergence times is notorious difficult and the field can be downright rancorous with some being accused of reading tea leaves and chicken entrails - interesting reading for personalities as much as the different scientific approaches. There are several different approaches to trying to estimate a divergence time among species, using calibration points usually anchored by fossil data. Molecular clock methods have problems sometimes producing extremely old dates that are quite hotly debated. In fungi we have a very few fossils (and their placement on the phylogeny is debated).
There are quite a few available methods for reconstructing divergence times including r8s and multidivtime which start with various types of trees and use calibration time points that are typically informed by fossil dates. The simplest approaches assume a molecular clock (rates are same across the tree) and then one only needs to calibrate the number of substitutions (or rate really) to time to determine how phylogenetic tree branch lengths map to time. The BEAST package also does phylogenetic inference and divergence time estimation (and provided the necessary analysis for exoneration of the Tripoli Six) across a sample of trees. BEAST (and MrBayes) use MCMC to sample the space of parameters and tree space to identify phylogenies and evolutionary parameters that explain the data (an alignment of sequences).
A paper from Akerborg and colleagues introduces a new approach that uses MCMC but apply a few twists, using a birth-death model that doesn't assume a molecular clock and employing a hill-climbing algorithm instead of MCMC to find parameter optima. They use a Maximum a posterior (MAP) framework which is more computational efficient than MCMC. They couple the MAP approach with a dynamic-programming approach that separates the estimation of rates (branch length) from the estimation of times (which often require assumption of a molecular clock). While I can't speak with much authority on the MAP approach or yet how well this compares on different datasets, it suggests a different method to tackle these problems. They authors point out one drawback with their approach is it only allows for derivation of point-estimates so statistical confidences like bootstrap support are not easily calculated through this approach. Their software, called PRIME is available here and I will be curious to see how it performs in other peoples' hands.
Akerborg, O., Sennblad, B., Lagergren, J. (2008). Birth-death prior on phylogeny and speed dating. BMC Evolutionary Biology, 8(1), 77. DOI: 10.1186/1471-2148-8-77
Categories: phylogenetics
Botany Photo of the Day: Chytrid
Posted on March 11th, 2008 by Jason Stajich · No Comments
Categories: chytridomycota
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

