The Hyphal Tip: Fungal Genomes and Comparative Genomics

Definitely worth listening to the RadioLab show episode "So-Called Life". The second act describes some "MIT bioengineering kids" who engineered sweet smelling E.coli. I'm sure some of them interviewed hang out at OWW, like Reshma. The sound effects for gene exchange and "The BioEngineers song" at the end of the 2nd act is definitely worth listening to.

Though less Fungal (and more fungal, if you'll grant me that) than most of the stories we cover, a recent analysis of the Diplonema papillatum mitochondria genome sequence is interesting nonetheless. The genome consists of over 100 chromosomes, each roughly 6 kilobasepairs (kbp) or 7 kbp in size. However, each chromosome contains only a short (less than 500 bp) gene encoding region. It appears that genes are scrambled, where modular genetic units are dispersed across many chromosomes. Curiously, despite having discontigous genes, cDNA sequencing identifies contiguous and properly ordered mRNA. So just how are scrambled genes expressed and asssembled?

PZ Meyers has a post summarizing of an older paper from Elliot Meyerowitz (2002) that comapares plant and animal development. In particular there is are some major themes summarized about how plants and animals form patterns and cell to cell signaling as part of development. What's missing is what we've learned about within group comparisons where there are multiple lineages of single-celled and multicelled

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

I had the pleasure of meeting Phil Ross, a SF area artist, last night at the BABS Darwin Day Celebration. He has been growing fungi in a variety of different ways to make living art in an project called 'Pure Culture'. He is using Ganoderma lucidum (a Polyporales fungus, which is being

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 ancestors.

Dettman, Anderson, and Kohn recently published a paper in BMC Evolutionary Biology on reproductive experimental evolution in two Neurospora crassa populations evolved under different selective conditions. This is a great study that complements work published last year in Nature on experimental evolution in Saccharomyces cerevisiae populations. Neurospora populations were evolved under high salt and low temperature and were started from either high diversity (interspecific crosses, N. crassa vs N. intermedia) or low diversity (intraspecific cross, two N. crassa isolates D143 (Louisiana, USA)and D69 (Ivory Coast)) as described in Figure 1. The experimentally evolved populations were then tested for asexual and sexual fitness (they were taken through complete meiotic cycle throughout the experiment to avoid insure there was selection on the sexual reproduction pathway.