All posts by Jason Stajich

Assistant Professor at UC Riverside

Whole genome tiling arrays

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.

PNAS Yeast Transcriptional map

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.

Experimental cooperative evolution

Blogging about Peer-Reviewed ResearchA paper in Nature this week describes how a few mutations can alter the interactions between species in a biofilm from competitive to cooperative system. This is a great study that goes from start to finish on studying community interactions, looking at an evolved phenotype, and understanding the genetic and physiological basis for the adaptation.

Acinetobacter sp. and Pseudomonas putida were raised in a carbon-limited environment with only benzyl alcohol as the carbon source. Acinetobacter can processes the benzyl alcohol, while P. putida is unable to. Acinetobacter takes up the bezyl alcohol and secretes benzoate that P. putida can then use as a carbon source. The research group propagated these in chemostats and looked at different starting concentrations of the organisms. They found that evolved P. putida had a different morphology and did several experiments to determine the relative fitness of the derived and ancestral genotype.

They went on to also map the mutations in P. putida and found two independent mutations in wapH (I think this is the right gene)—a gene involved in lipopolysaccharide (LPS) biosynthesis. They then engineered the ancestral strain to have a mutation in P. putida and found the rough colony phenotype morphology indistinguishable from the strain derived from experimental evolution.

There are various evolutionary and niche adaptation implications arising from this study. One application to mycology is to how lichens evolved in that an algael cell and a fungal cell must communicate and cooperate.

Authors

The current contributors to this blog are

Jason Stajich maintains this blog site, a wiki for collaboration, and software and is an Assistant Professor University of California, Riverside in the Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology.  He also provides some genome browsers for fungal genomes as part of his research and in collaboration with the community.

Occasional contributors
Thomas Sharpton is a postdoctoral fellow at University of California, San Francisco in the Gladstone Institute
Chris Villalta, grad student at UC Berkeley
Balaji Rajashekar was previously at Lund University

We welcome other participants. If you would like to contribute content to this site or to our wiki, please sign up for an account and contact Jason by email.

Not one, but two Aspergillus niger genome sequences

Blogging about Peer-Reviewed ResearchA.niger growing on plate (this is not the sequenced strain)The JGI has previously released A. niger strain ATCC 1015 sequence in November 2005. ATCC 1015 is used in industrial production of citric acid as it is one of the best producers of citric acid. In Nature Biotechnology a Dutch team has published the sequence of another strain, CBS 513.88 which is an early ancestor of ATCC 1015 used in industrial enzyme production.

Genomes of honeybee pathogens

A.apisBlogging about Peer-Reviewed ResearchThe Baylor sequencing center has published the genome of two honey bee pathogens. Recently Baylor and collaborators published a slew of honey bee genome papers and it is great that they have also chosen to follow up on the parasites as well.

The group published the genomes of the bacteria pathogen Paenibacillus larvae and fungal pathogen Ascosphaera apis. A. apis is in the Onygenales clade which also includes the fungal human pathogens Coccidioides, Histoplasma, and Blastomyces.

Currently the genome annotation is limited to the bacterial genome where many ab initio gene prediction programs exist and no annotation is provided for A. api. We should be able to apply gene prediction parameters trained from other Onygenales fungi to get a resonable annotation. Study of this pathogenic genome may also provide insight into the evolution of this clade of fungi which contains most of the primary fungal pathogens of humans.

Tripartate symbioses with fungi

Ants, fungi, and bacteria

I have to admit that I am fascinated by co-evolution of symbiotic and mutalistic systems. A review by Richard Robinson gives an overview. A great example is the mutalism between ants and fungi where the ants cultivate the fungi for food. There are more layers to the relationship as a fungal parasite (Escovopsis) attacks the cultivated fungi, and a bacteria. Several researchers have studied the coevolution of these studies including Ulrich Mueller and Cameron Currie. Currie and Mueller have published several great studies describing the patterns of coevolution and the nature of the cooperation.
Continue reading Tripartate symbioses with fungi

All hail the rusts

pucciniaThe FGI and the Broad Institute have released the 7X genome assembly of Puccinia graminis f. sp tritici in roughly 4500 contigs. This represents the first rust fungus to be sequenced and the second Urediniomycete that has been sequenced, Sporobolomyces roseus being the first. This rust fungus is “the causal agent of stem rust, has caused serious disease of small cereal grains (wheat, barley, oat, and rye) worldwide.”

Phycomyces Genome Release 1

phycomycesThe JGI has released the Phycomyces blakesleeanus genome. This represents the second Zygomycete genome sequence that has been released in addition to Rhizopus oryzae that was released by the Broad Institute last year. We are now getting a better look at the basal fungal genomes including the Chytrids and Zygomycetes. Much more on specifics of Phycomyces biology and history are on this site run by the group organizing the genome analysis.

I find one of the most interesting things about P. blakesleeanus is its phototropism. We know light sensing is controlled, in part, by the gene white-collar 1. A homolog of this gene in Neurospora crassa is involved as an oscillator circadian rhythm. Of course many more genes are involve in pathways for light sensing including some really old proteins like phytochromes.

There will be a lot of cool analyses to do with this genome beyond phototropism. I am looking forward to seeing what gene families are unique and expanded in this species relative to the other zygomycete. It also looks like it is quite intron rich much like the Basidiomycetes, further supporting the idea that fungi had intron rich ancestors.