Category Archives: comparative

Evolution of aflatoxin gene cluster

Blogging on Peer-Reviewed ResearchIgnazio 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

Evolution of PEX genes

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
Woronin bodies in A. nidulans from Momany et al, Mycologia 2002

Continue reading Evolution of PEX genes

Orthology detection software

Blogging about Peer-Reviewed Research 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.

Proteins Evolve Differentially in Saccharomyces

Blogging about Peer-Reviewed ResearchPerhaps 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.

Genome resources for Candida species

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.

Making the Revolution Work for You

In a recent Microbiology Mini-Review, Meriel Jones catalogs both the potential benefits and problems that arise from fungal genome sequencing. Using the nine genomes (being) sequenced from the Aspergillus clade, Jones addresses several issues tied to a singular theme: if we are to unlock the potential that fungal genome sequencing holds, both academically and entrepreneurially, then a more robust infrastructure that enables comparative and functional annotation of genomes must be established.

Fortunately, like any good awareness advocate, Jones points us in the direction of e-Fungi, a UK based virtual project aimed at setting up such an infrastructure. Anyone can navigate this database to either compare the stored genomic information or evaluate any fungus of interest in the light of the e-Fungi genomic data. The data appears to be precomputed, similar to IMG from JGI, so there are inherent limitations on the data that one can obtain. However, tools such as these put important data in the hands of expert mycologists that can turn the information into something biologically meaningful.

As Jones points out, this is just the beginning. If fungal genomes are to live up to their promise, they must engage more than just experts at reading genomes.

Not one, but two Aspergillus niger genome sequences

Blogging about Peer-Reviewed ResearchA.niger growing on plate (this is not the sequenced strain)The JGI has previously released A. niger strain ATCC 1015 sequence in November 2005. ATCC 1015 is used in industrial production of citric acid as it is one of the best producers of citric acid. In Nature Biotechnology a Dutch team has published the sequence of another strain, CBS 513.88 which is an early ancestor of ATCC 1015 used in industrial enzyme production.