The Hyphal Tip: Fungal Genomes and Comparative Genomics

The genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings.  The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons

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.  

Tom Bruns, Martin Bidartondo and 250 others sent a letter to Science describing the current problems with fixing annotation in GenBank. There is an entertaining accompanying news article that interviews several people about the problem of updating annotation and species assigned to sequences in the database. In particular the problem for mycologists that many fungi found from metagenomic approaches are only identified through molecular sequences and having the wrong species associated with a sequence can be difficult when studying community ecology composition.  This problem is not limited to fungi by any means, but recent reports find as many as 20% of fungal Intergenic Spacer (ITS) sequences are mis-attributed to the wrong species. 

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.

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 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.

While many strains of S. cerevisiae are being sequenced, a single strain, YJM789, isolated from the lung of an AIDS patient was sequenced a few years ago at Stanford and published this summer. The genome was described in a paper entitled "Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789". The authors find a few notable rearrangements and unique genes in this strain as compared to the lab and type strain S288C. They find examples of horizontally transferred genes or potentially genes (like RTM1) which are being exchanged among individuals in the population and just not found in first sequenced strain. There are several other genome architecture observations including numbers of indels and highly polymorphic (and thus different from S288C) ORFs. In general the chromosomes are co-linear but they find some rearrangements. One of the main trains of a human pathogenic fungi, which some people will argue aren't really pathogenic since the host must be severely immunocompromised to infect, is the ability to grow at high or body (37 C) temperatures. Most fungi can't survive at this temperature, but this trait is a necessary condition for fungi like Cryptococcus neoformans, Aspergillus fumigatus, and the pathogenic Candida species like C. albicans to infect and potentially overwhelm a host. Previous work from many of the same authors used a QTL approach to map the high temperature phenotype in a clinical strain Saccharomyces using a new genetic technique called reciprocal-hemizygosity to dissect the QTL. This is only the second actual publication of the genome of another strain of Saccharomyces cerevisiae even though there have been several papers profiling rates of evolution in the lab and wild strains S288C, YJM789, and RM11-1A (Gu 2005, Ronald et al 2006) before the final genome paper was published. I doubt we'll keep seeing papers about a single strain sequenced when there is already a reference strain. Instead papers about clusters of strains or closely related species such nearly complete work in other Saccharomyces strains, Coccidioides and Neurospora will probably be the norm. This paper is available as Open Access through PNAS which I applaud the authors for. However, the paper concludes with a paragraph that starts

"Finally, we made the YJM789 genome a free-to-access resource that marks an initial step toward a more complete set of reference sequences for the S. cerevisiae species"

While I am happy to see the sequence resource freely available now, I guess I've come to expect this with any genome publication. The sequence has been available with some restrictions at least since 2003 before the genome was published in a journal. I am unsure why this needs to be championed in the conclusion, shouldn't it be available as a consequence of how it was funded or am I expecting too much?

"This work was supported by National Institutes of Health Grants HG02052 (to R.W.D.), GM068717 (to R.W.D. and L.M.S.), and HG000205 (to R.W.D. and L.M.S.);"

There is more discussion of the project and its future at the Stanford site.

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".

A paper by Martin Aslett and Val Wood indicate that the fission yeast community is approaching 100% coverage of a GO annotation for every gene in the S. pombe genome. Only Ashbya gossypii has a smaller genome in the fungi (see a recent paper