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
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
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.
Hyphoid Logic rips on the Alameda Sun for calling Coccidoidies a virus.
The NY Times has an article on the high rate of Coccidioides incidence at the state prison in Pleasant Valley, California. The infection rate has been documented by Pappagianis et al in an in-depth study of Coccidioidomycosis in the California state prisons. The disease has stalled some plans for constructing a new prison the edge of the San Joaquin Valley so the state is definitely taking note.
Also see Figure here with prettier links.
I’m excited about our projects to tackle the evolution of the Onygenales fungi.
I just remembered to look and see what was going on with the Blastomyces genome sequencing at WashU. I checked and the Blastomyces dermatitidis genome sequence assembly version 3 was released in October 2007 and ESTs via 454 and ABI technologies are all available from WUSTL Genome Sequencing Center.
With the Broad Institute release this week of the Paracoccidioides genome sequence, the 10 Coccidioides strain genomes + 1 C. posadasii strain from JCVI/TIGR, 3 strains of Histoplasma capsulatum (both WUSTL and Broad), and the in-progress dermatophyte for Trichophyton and Microsporum sequences that are being generating through the FGI at Broad we have incredible genome coverage of this group of dermatophyte, keratin loving, and often animal pathogenic fungi.
I know I’ve been accused of being too positive announcing these things, but I do think analyses here are going to be as rich for comparisons as any old 12 flies.
The Broad Institute has made available additional genomes of strains of Coccidioides immitis and C. posadasii. There are now genome sequences for 4 strains of C. immitis sequenced and 3 strains of C. posadasii including the C735 strain from the JCVI/TIGR. including the reference strain RS that is assembled into 7 supercontigs (there are probably 5 chromosomes) and annotated with ~10,000 genes. However we think at least ~1-2k of the annotated genes in strain RS are likely reptitive sequences and not real genes based on comparisons with the TIGR annotations of C. posadasii C735 strain and de novo repeat finding and analysis – John talked about this in his talk at Asilomar.
Thse available strain sequences are going to allow for some interesting analyses that have yet to be applied in fungi. This includes doing some whole genome scans for selection using more sensitive population genetic tests than the gross-level non-synonymous /synonymous ratio tests that we’ve been relegated to with the current comparisons and it is starting to feel a bit like when “all you have is a hammer…”. Now all we have to do is get the whole genome multi-strain alignment quirks worked out and probably have to do our own quick annotation since only the two reference strains are annotated.