A new paper from the Zilberman lab at UC Berkeley shows the application of high throughput sequencing to the study of DNA methylation in eukaryotes. They generate an huge data set of whole genome methylation patterns in several plants, animals, and five fungi including early diverging Zygomycete.
The work was performed using Bisulfite sequencing (Illumina) to capture methylated DNA, RNA-Seq of mRNA. The also performed some ChIP-Seq of H2A.Z on pufferfish to look at the nucleosome positioning in that species. For aligning the reads, they used BowTie to align the bisulfite sequences (though I’d be curious how a new aligner, BRAT, designed for Bisulfite seq reads would perform) to the genome. They also sequenced mRNA via RNA-Seq to assay gene expression for some of the species.
They find several interesting patterns in animal and fungal genomes. I’ll highlight one in the fungi. They find an unexpected pattern in U. reesii of reduced CGs in repeats, which shows signatures of a RIP-like process, are also methylated. This finding is also consistent with observations in Coccidioides (Sharpton et al, Genome Res 2009) that showed depleted CGs pairs in repeats. Since the phenomenon is also found in Coccidioides genomes this methylation of some repeats is likely not unique to U. reesii but may be important in recent evolution of the Onygenales fungi or the larger Eurotiales fungi. There are several other interesting findings with the first such study that shows methylation data for Zygomycete fungi and a basidiomycete close to my heart, Coprinopsis. It will be interesting is to dig deeper into this data and see how the patterns of methylation compare to other genomic features and the mechanisms regulating methylation process.
Zemach, A., McDaniel, I., Silva, P., & Zilberman, D. (2010). Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation Science DOI: 10.1126/science.1186366
In a letter to the editor to the journal Nature, regarding the recently discovered/induced sexual stage in Aspergillus fumigatus, David Hawksworth argues that using the separate names for sexual (teleomorph) and asexual (anamorph) stages is confusing and unnecessary in this context. The name Neosartorya fumigata is given to the sexual stage which was produced from two individuals which were both A. fumigatus. The letter writer makes the point that referring to a new name for the sexual stage when we already know what its anamorph is seems superfluous and overly confusing. He gives the analogy of Aspergillus nidulans where its teleomorph Emericella nidulans is “largely ignored”.
The double names for something which is the same species (i.e. has the same genomic sequence) is certainly a confusing aspect of mycology. It stems from the morphological description of species and that before DNA or molecular approaches to identification it was difficult to connect the anamorph and teleomorph stages unless you could induce the entire lifecycle in the laboratory. I think that the same name for homologous structures from different phyla is also equally confusing, but necessary aspect of how things are currently named and classified.
What researchers should described the sample/individual they are using for experiments in their manuscripts is important to avoid confusion and for readers so I think Prof Hawksworth makes an important point especially when discussing something where the anamorphs and teleomorphs are unified. Certainly an agreed upon protocol here would be quite helpful of what to preferably use when the stages have been connected.
Hawksworth, D. (2009). Separate name for fungus’s sexual stage may cause confusion Nature, 458 (7234), 29-29 DOI: 10.1038/458029c
Shepard Fairley has gotten alot of notice lately for his Obama art that has been replicated pretty much everywhere. I mocked up a homage to his earlier street art — here we’ll discuss the growing Aspergillus genome posse.
But the work from mainly the JCVI, Broad Institute, JGI, NITE, and Sanger centre has generated an excellent collection of genome sequences for the Eurotiales clade (feel free to get a login for the wiki and add other that are missing). The Aspergillus community now has a AGD – Aspergillus Genome Database project that includes a curator of genome annotation (they are hiring) and presumably literature in the SGD and CGD model of curation.
I think a lot of other projects have a Posse too (or maybe just a loosely organized band) in terms of a community of people working on related species and willing to work together to coordinate. As these sort of “clade” databases start to develop we will have better clusters of information that can be mapped among multiple species.
Eventually I hope this will spur efforts for more coordinated genome databases for comparative genomic and transfer of known gene and functional information between experimental systems. The efforts really require coordination or centralization of the data so that gene models can be updated as well as orthologs and phylogenomic inference of function.
A manuscript at Nature AOP details the success of the Dyer lab and collaborators in encouraging Aspergillus fumigatus to complete the sexual cycle under observable (e.g. laboratory) conditions. The authors are the teleomorph (sexual or perfect) stage Neosartorya fumigata for a fungus that had been previously only had an observed anamorphic stage. A. fumigatus can reproduce asexually forming structures called conidiophores which produce asexual spores called conidiospores (or mitospores as they are produced via mitosis) define the anamorph or imperfect stage, but no sexual structures such as cleistothecia that produce the packaged sexual products as ascospores. See a presentation by David Geiser (archived at the Aspergillus website) for more detail on some of the morphological and phylogenetic characters that unify the group of Eurotiales fungi.
Like several other groups of fungi, A. fumigatus was presumed to have a putative cryptic sexual stages inferred from population genetic evidence of sexual recombination, but until no telemorphs had been observed. In addition, an observed perfect stage doesn’t necessarily indicate it is easy to induce mating in laboratory conditions. Complicated media including the ever stressful V8 juice was needed to induce mating in the basidiomycete yeast Cryptococcus neoformans (Erke, J Bacteriol 1976). In fact, Christina Hull’s lab has shown we still don’t even know what ingredients in V8 juice even induce mating (Kent et al, AEM 2008)! Other fungi including Coccidioides have been implicated as cryptically sexual (Burt et al, PNAS 1996) but no one has been able to induce mating in laboratory conditions. In this case a petri plate with a individual of each mating type (since this is a heterothallic fungus), and a series of different media conditions provided an environment suitable for mating to occur.
The work in this paper follows from their previous work identifying isolates of different mating types (Paoletti, Current Biol, 2005). The discovery of sexual stage for Aspergillus fumigatus (which Bret cannot pronounce) is a boon for molecular geneticists in construction of knockout strains and ability to follow recombination. While A. nidulans is a sexual species and model system for genetics, it is useful to have more tools to directly manipulate A. fumigatus and directly test hypotheses about genes involved in pathogenicity.
This observation of meiosis in the laboratory is also is interesting to considered in light of work that RIP is active in other Aspergillus species (and also see this post) suggesting that RIP may be operating under meiotic conditions.
Isolates of different mating types have also been described for the putatively asexual Coccidioiodes (Mandell et al, EC 2007; Fraser et al, EC 2007) so it remains a possibility that we can also induce sexual recombination in laboratory conditions in this fungus.
Céline M. O’Gorman, Hubert T. Fuller, Paul S. Dyer (2008). Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus Nature DOI: 10.1038/nature07528
BBC news and GTO report the sequence of P. chrysogenum, will be published in October in Nat Biotechnology in a project based at the biotech company DSM. P. chrysogenum being the mold that fortuitously contaminated Dr Fleming’s bacterial plates.
The 13,500 reported genes in the press release is quite bit larger than relatives in the Aspergillus clade (~10,000 genes) so it will be intriguing to see what’s going on here and if there will be interesting examples of horizontal transfer like what has been investigated in Aspergillus oryzae. I am unclear as to whether the selected strain is a wild isolate or represents an industrial strain, but look forward to reading the full account of the genome.
Factoid – Most of the industrial fungal genome papers have seen publication in Nature Biotechnology (Aspergillus niger, Trichodermera reesei, and Phanerochaete chrysosporium).
Edit: 1-Oct-2008, Jonathan Badger, an author on the paper, blogs about the paper and links to the pre-print available on NBT site.
The first of several dermatophyte fungal genomes, Microsporum gypseum, has been released at the Broad’s Dermatophyte site. Two Tricophyton species and another Microsporum genome should follow soon. These dermatophyte fungi are Onygenales (Ascomycota) fungi (like Coccidioides and Histoplasma), although their placement in the phylogenies shown in the whitepaper and related review paper is a bit ambiguous. I’m sure that can be improved with a few more gene sequences gleaned from the genomes.
The 23 Mb M. gypseum genome is a bit smaller than the sizes of C. immitis (28 Mb), H. capsulatum (32 Mb), or Paracoccidioides brasiliensis (29 Mb). While no annotation is currently available for the M. gypseum genome, this genome will help in establishing what genes were ancestral in the Onygenales and comparing patterns of gene family gains and losses in fungi that specialize on animal hosts.
Some more comparison across different kinds of dermatophyte fungi that are very distantly related like dandruff causing fungus Malasezzia globosa (Basidiomycota) will be really interesting as well.
Thanks Joe H and FGI folks for passing along announcement and to the Broad/FGI folks for the work to make this sequence available.
We’re excited that a Penicillium marneffei grant to Mat Fisher and collaborators has been funded by the Welcome Trust. It includes a collaboration with Bignell Lab at Imperial College, our lab, JCVI, and Univ of Melbourne. This project will explore functional and comparative genomics approaches to studying the fungus which primarily infects immune compromised individuals in south-east asia where it is found associated with bamboo rats.
Scientists at Imperial College London have received almost £350 000 from the Wellcome Trust, the UK’s largest medical research charity, to study Penicillium marneffei, the only Penicillium fungus to cause serious disease in humans. The researchers aim to find out what makes this particular fungus pathogenic.
Read the rest of the release.
A paper in Science from Jason Crawford and colleagues explores the function of polyketide synthetases (PKS) in the synthesis of the secondary metabolite and carcinogen aflatoxin. Previous work (nicely reviewed in the fungi by Nancy Keller and colleagues) has shown the the PKS genes have several domains. These domains include acyl carrier protein (ACP), transacylase (SAT), ketosynthase (KS), malonyl-CoA:ACP transacylase (MAT), “product template” PT, Aand thioesterase/Claisen cyclase (TE/CLC). These domains make up PksA, but the specific role of each domain’s in synthesis steps has not been fully worked out. Understanding this process and the specificity of the chemical structures that are created can help in redesign of these enzymes for synthesis of new molecules and drugs.
Then authors cloning and combining the domains from a cDNA template of pksA [accession AY371490] (from Aspergillus parasiticus) into various combinations and then evaluated the synthesized products via HPLC. This deconstruction of a complicated protein and its domains is a great example of functionally mapping the role of each part of the enzyme and integrating with the biochemistry of the synthesized products. The findings of this research also mapped a role for the PT product template domain which could suggest where modifications could be made to tweak the synthesized products by these enzymes.
Crawford, J.M., Thomas, P.M., Scheerer, J.R., Vagstad, A.L., Kelleher, N.L., Townsend, C.A. (2008). Deconstruction of Iterative Multidomain Polyketide Synthase Function. Science, 320(5873), 243-246. DOI: 10.1126/science.1154711
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. Continue reading
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.