By Jason Stajich, on June 13th, 2009
Genome sequencing is underway on several early branches in the Opisthokont and some related linages as part of the “Origins of Multicellularity” project at the Broad Institute (BI) include some recently made available assemblies for:
Allomyces macrogynus (Blastocladiomycota “Chytrid”)
Capsaspora owczarzaki (Ichthyosporea)
Already available data from
Monosiga brevicolis (JGI)
Batrachochytrium dendrobatidis (JGI, BI) (Chytridiomycota)
Still in progress (BI)
Amastigomonas sp
Amoebidium parasiticum
Nuclearia simplex
Salpingoeca or [...]
By Jason Stajich, on December 26th, 2008
A recent paper in MBE presents evidence that the Taphrinomycota (containing S. pombe and Pneumocystis) are in fact a monophyletic group. This is considered an early branch in the Ascomycota with the Pezizomycotina (filamentous ascomycete fungi like Neurospora and Aspergillus) and Saccharomycotina (fungi mainly with yeast forms including Candida and Saccharomyces). The monophyly of Taphrinomyoctina fungi is something that has been fairly accepted but there are a few publications reporting conflicting evidence in some sets gene trees. This conflict is most likely due to Long Branch Attraction (LBA) and the Philippe lab has long worked on this problem of LBA working to develop tools like PhyloBayes that attempt to correct for LBA with a parameter rich model and using lots of data (like whole [...]
By Jason Stajich, on April 9th, 2008
We may have to reevaluate whether Saccharomyces cerevisiae alone is the species used to brew beer. A paper from Gonzalez et al describes results from PCR-RFLP comparison of 24 brewing strains identifies evidence for S. cerevisiae x S. kudriavzevii hybrids. Although this hybridization is not unprecedented, most seem to be related to cultivated brewing or [...]
By Jason Stajich, on February 17th, 2008
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
By Jason Stajich, on February 8th, 2008
A 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 [...]
By Jason Stajich, on July 30th, 2007
Back from ISMB/ECCB and a mountain of things left undone that somehow still need doing … including a quick entry about what was interesting at the [...]
By sharpton, on March 30th, 2007
Perhaps not a surprise to anyone that has dabbled in evolutionary analysis of proteins, Kawahara and Imanishi (BMC Evolutionary Biology 2007) confirm that not every protein evolves via a molecular clock in Saccharomyces
sensu scricto. Using everyone’s favorite evolutionary tool, PAML, the authors identify protein lineages via a whole genome scan that evolve relatively slow [...]
By Jason Stajich, on March 18th, 2007
The Candida clade of Hemiascomycete fungi have received much attention from funding bodies so that many genomic and experimental resources are available address questions of pathogenecity and industrial applications of these species.
The Candida genus
Traditionally, species of yeasts that were thought to be asexual were given the genus name Candida. This has lead to Candida being a sort of taxonomic rubbish [...]
