The Hyphal Tip: Fungal Genomes and Comparative Genomics

The [[Trichoderma reesei]] genome paper was recently published in Nature Biotechnology from Diego Martinez at [[LANL]] with collaborators at [[JGI]], [[LBNL]], and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol production.

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

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.

On the cover of this week's Nature is a picture of Phycomyces blakesleeanus highlighting the discovery of the MAT locus in this Zygomycete fungus from Alex Idnurm and Joe Heitman and colleagues. While it was previously known that Zygomycetes (the Orange lineage represented by R. oryzae in the tree below) mate, the specific locus has until now, never been discovered. The authors in this study identified the MAT locus through a sequence search looking for HMG-box genes knowing that these are found the Mating Type locus in Basidiomycetes and Ascomycetes. They confirmed the identity through a through set of experiments that included PCR, sequencing and crosses of (+) and (-) strains of P. blakesleeanus, and Southern blots.

The Willi Hennig Society, homebase for all good cladists, has subsidized the license fee for TNT so that it is now a freely available program (although it is not open-source). TNT implements phylogenetic analysis under parsimony with a fast tree searching algorithm. I believe TNT was one of the software

Dave Hibbett wrote a great article for Mycological Research that describes the current state of systematics and evolutionary studies of morphology in mushroom-forming Agaricomycete fungi. His article, dedicated to the late, great mycologist Orson K Miller, Jr and entitled "After the gold rush, or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century" describes the how classification and systematics has changed in the last two hundred years and macromorphology to the more than "108,000 nucleotide sequences of ‘homobasidiomycetes’, filed under 7300 unique names."

The article contains some beautiful pictures many of which are taken from some of the eminent mycological photographers and mycologists Michael Wood and Taylor Lockwood.

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.

Fungi, like most organisms, take an active role in finding food for survival. When thinking about hostile takeovers by fungi, one probably thinks about mycelia growing towards nutrients, rotting plant matter, the ability to extract nutrients from a living host, or perhaps producing toxins or secondary metabolites that can affect the host. However, some fungi can take an even more active role and trap their animal hosts (when that animal isn't much bigger than you). A paper from earlier this year on "Evolution of nematode-trapping cells of predatory fungi of the Orbiliaceae based on evidence from rRNA-encoding DNA and multiprotein sequences" describes the evolutionary history of a group of fungi able to trap and eat nematodes. Nematode trapping fungi have been investigated experimentally since at least the 30s (Drechsler, Mycologia. 1937, Drechsler, J Wash Acad Sci. 1933), and some more recent studies of the relationship of the groups (Rubner, Studies in Mycology. 1996). In the recent PNAS paper, the authors used multi-locus sequencing to reconstruct a phylogeny and history of large group of carnivorous fungi and reconstruct the ancestral history the prey trapping mechanism of either through constricting rings or adhesive traps. They were able to reconstruct the likely order of the evolutionary steps needed to make the stalk and trapping cells. They found that the most common type of trap, an Adhesive Network, was the earliest evolved trap. Some movies also demonstrate how these fungi make their living.

Michigan State researchers Heather Hallen and Jonathan Walton have reportedly cloned genes from Amanita for alpha-amanitin (mispelled as alpha-aminitin in NYTimes article) which inhibits RNA polymerase II and phallacidin which inhibits actin filament polymerization. The gene sequences are in GenBank for those itching to look at evolutionary relationships of these genes in other fungi. This is unfortunately another annoying example of science-by-press release where the PNAS publication is not available but the press release and NYtimes article are, but that shouldn't take aware from a cool result. We also had to wait a week after the dandruff genome announcement to read that paper, I hope the PNAS press-release publication-release timeline gets synchronized soon... Update: Gene family encoding the major toxins of lethal Amanita mushrooms manuscript is available now. A writeup about the A. bisporigera "destroying angel" shown here can be read at the Cornell Mushroom blog and the deadly consequences of ingesting it. [Thanks ShannonS via FredS]

Robin reviews recent Nature paper by Ilan Wapinski et al describing the orthogroups they built from multiple fungal genomes. I've been remiss in reviewing the paper myself, but they've created an important resource in the SYNERGY tool for orthology identification and a database of orthologs of some ascomycete fungi. I am excited there is a level of interest in the properties of gene duplication and how this may be an important aspect of adaptation and evolution. The Cornell Mushroom blog has a nice treatment of the maize pathogen and Mexican delicacy Ustilago maydis corn smut. Chris and Tom took some more Coprinus pictures while I was away from the lab.