The Hyphal Tip: Fungal Genomes and Comparative Genomics

This month's Genetics has a series of articles exploring the genome (published last year & freely available at Science) of the green algae [[Chlamydomonas reinhardtii]]. These manuscripts are primarily genome analyses making for a very bioinformatics focused issue of Genetics. Some of the highlights include:

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.

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.

A paper in PLoS Biology from Sandy Johnson's lab entitled "Interlocking Transcriptional Feedback Loops Control White-Opaque Switching in Candida albicans" discusses phenotype switching in the human pathogenic fungus Candida albicans. Why is the important?

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".

Your eye contains the same genetic content as your fingernail, but these two tissues look nothing alike. One significant cause of this difference is the tissue specific regulation of the genes in the genome. In some tissues in your body, a gene may be expressed (transcribed) while that same gene may be silent in another tissue type.

A recent paper describes the discovery of 9 new introns in Saccharomyces cerevisiae by Ron Davis’s group at Stanford, using high density tiling arrays from Affymetrix. The arrays are designed for both strands allow the detection of transcripts transcribed from both strands. The arrays were also put to work by the Davis and Steinmetz labs to create a high density map of transcription in yeast and for polymorphism mapping from the Kruglyak lab. Whole genome tiling arrays have also been employed in other fungi. For example, Anita Sil’s group at UCSF constructed a random tiling array for Histoplasma capsulatum and used it to identify genes responding to reactive nitrogen species. A similar approach was used in Cryptococcus neoformans to investigate temperature regulated genes using random sequencing clones. As the technology has become cheaper, it may become sensible to use a tiling array to detect transcripts rather than ESTs when attempting to annotate a genome. In the Histoplasma work transcriptional units could be identified from hybridization alone. Some of the algorithms will need some work to correct incorporate this information, and the sensitivity and density of the array will influence this. These techniques can be part of a resequencing approaches or fast genotyping progeny from QTL experiments when the sequence from both parents is known (or at least enough of the polymorphims for the genetic map). What is superior about the current Affymetrix yeast tiling array is the inclusion of both strands. This allows detection of transcripts from both strands. Several anti-sense transcripts in yeast have been discovered recently including in the IME4 locus through more classical approaches, but perhaps many more await discovery with high resolution transcriptional data from whole genome tiling arrays.