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.”
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”.
A recent PLoS One article “A Genetic Code Alteration Is a Phenotype Diversity Generator in the Human Pathogen Candida albicans” finds some pretty dramatic changes in gene expression and phenotypes by replacing the tRNAs for CUG back to Leucine (Leu; in the standard genetic code) from their meaning of Serine (Ser) in these Candida species. The CUG codon transition in some Candida spp has been of interest since it is an example of a recent change in the genetic code and provides a comparative system to study the mechanism and genome changes of how a genetic code shift is manifested.
Few organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise. What is curious is the large number of yeast genes for which we’ve been unable to characterize. Of the ~6000 genes currently identified in the yeast genome, 1253 have no verified function (for the uninclined, this is roughly 21% of the yeast proteome). Egads! If we can’t figure this out in yeast, what hope do we have in non-model organisms?Lourdes Peña-Castillo and Timothy R. Hughes discuss this curious observation and its cause in their report in Genetics.
Ignazio Carbone and colleagues published a recent analysis of the evolution of the aflatoxin gene cluster in five Aspergillus fungi entitled “Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster” in BMC Evolutionary Biology. The authors were able to identify seven modules pairs of genes whose history of duplication were highly correlated. Several genomes of Aspergillus have been sequenced along with more Eurotioales fungi. Continue reading Evolution of aflatoxin gene cluster
A nice evolutionary analysis of peroxin genes entitled PEX Genes in Fungal Genomes: Common, Rare, or Redundant in the journal “Traffic” from Kiel et al out of the University of Groningen in The Netherlands. Within a species, the genes in the PEX family are not necessarily phylogenetically related to each other, but instead are all named as to how they were discovered in mutant screens, most of which were done in S. cerevisiae.
Peroxisomes are interesting because they are necessary for some biochemical reactions (fatty acid metabolism). In filamentous fungi there are additionally specialized peroxisomes called Woronin bodies that plug the septal pore that separates individuals cells in a hyphae. These are specific to filamentous fungi so it is interesting to contrast the numbers and types of genes in the PEX family that are present as determined from the genome sequences. To relate this to human biology, the authors suggest that understanding the complex phenotypes of human peroxisome biogenesis disorders (PBD) will be helped through the study of the disruptions of PEX genes in various filamentous fungi. Interestingly, they find that nearly all PEX genes are present in all fungi, yeast and filamentous alike, although there may be additional genes unidentified.
Woronin bodies in A. nidulans from Momany et al, Mycologia 2002
A paper in PLoS One, Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes, reports a new approach to assess the performance of automated orthology detection. These authors also wrote the OrthoMCL (2006 DB paper, 2003 algorithm paper) which uses MCL to build orthologous gene families. The authors discuss the trade-offs between highly
sensitive specific tree-based methods and fast but less sensitive approaches of the Best-Reciprocal-Hits from BLAST or FASTA or some of the hybrid approaches. The authors employ Latent Class Analysis (LCA) to aid in “evaluation and optimization of a comprehensive set of orthology detection methods, providing a guide for selecting methods and appropriate parameters”. LCA is also the statistical basis for feature choice in combing gene predictions into a single set of gene calls in GLEAN written by many of the same authors including Aaron Mackey.
I’ve been reading a lot of orthology and gene tree-species tree reconcilation papers lately, some are listed in Ian Holmes’s group as well as listing some of the software on the BioPerl site. This also follows with on our Phyloinformatics hackathon work which we are trying to formalize in some more documentation for phyloinformatics pipelines to support some of the described use cases. I’m also applying some of this to a tutorial I’m teaching at ISMB2007 this summer.
Perhaps not a surprise to anyone that has dabbled in evolutionary analysis of proteins, Kawahara and Imanishi (BMC Evolutionary Biology 2007) confirm that not every protein evolves via a molecular clock in Saccharomyces sensu scricto. Using everyone’s favorite evolutionary tool, PAML, the authors identify protein lineages via a whole genome scan that evolve relatively slow or fast compared to the rest of the clade. Some changes even appear to be due to the invisible hand of natural selection and independent of the complications that may have arisen during the whole genome duplication in the ancestor of this clade.
It has been previously speculated that, either upon protein duplication or change in the selective regime of the environment, a protein may rapidly evolve at speciation and then, upon obtaining a new, important function, slow down it’s evolutionary rate to a clock-like tempo. One of the black boxes in this hypothesis is whether or not closely related proteins can rapidly diverge. While the authors are not able to identify a mechanism explaining how, their study demonstrates the plausibility of this hypothesis. However, it remains uncertain if proteins that exhibit rapid divergence will subsequently slow down their evolutionary rate later in time.
It’s good to see evolutionary analysis being applied to fungal genomes. With so many sequenced species spanning a great range of phylogenetic distance, the fungal kingdom is poised to provide great insight into the evolution of eukaryotes.
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 we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.
The Candida clade of Hemiascomycete fungi have received much attention from funding bodies so that many genomic and experimental resources are available address questions of pathogenecity and industrial applications of these species.
The Candida genus
Traditionally, species of yeasts that were thought to be asexual were given the genus name Candida. This has lead to Candida being a sort of taxonomic rubbish bin as this system of classification breaks down when asexuality arises more than once (creating homoplasy). For example, the asexual Candida glabrata is found within the Saccharomyces clade when molecular phylogenetics is applied. The problem lies in that many of these species appear very similar visually and microscopically and so there had not been enough phylogenetically informative phenotypic characters to easily classify them further. With the use of molecular phylogenetics the classifications have been improved as shown in several studies, however we retain the historical nature of the genus and species names for these organisms for the time being even though the phylogenetic diversity of species in the “genus” is much broader than other genus-level classifications. It will be interesting to see whether taxonomic proposals like PhyloCode or traditional revisions of the species names will provide new names for the group.
The Candida Genome Database (CGD) sister to the Saccharomyces Genome Database (SGD) provides resources for phenotype and sequences related to human commensal and dimorphic fungus Candida albicans. A recent paper by Arnaud et al describes the resources that are available through their website. An essentially completed C. albicans diploid genome with curated gene models and annotations provides an essential resource for this model pathogenic system. In addition to the SC5314 strain of C. albicans the white-opaque (WO) strain can switch between different colony morphologies – white and smooth or gray and rod shaped.
6 additional species have had their genomes in the Candida clade have had their genomes sequenced including Pichia stipis, Debaryomyces hansenii, Candida lusitaniae, Candida tropicalis, Candida guilliermondii, and Lodderomyces elongisporus. These resources will hopefully shed some light on the importance and mechanisms for dimorphic switching in the pathogen C. albicans, the importance and evolution of alternative codon usage in the clade, and better usage of the industrial yeasts like P. stipitis and D. hansenii.