Category Archives: phylogeny

One Fungus, One Name

The naming of organisms is an important part of how we communicate. When a fungus is found, be it a mycelium from a rotting fruit, a mushroom from the forest, or something growing on a petri dish, we have used morphological and other phenotypic characteristics to group them together and identify if it is an already known species or a new one. However, some fungi have very different shapes and forms that occur during asexual and sexual (after mating with a partner) stages, some incredible elaborate and even (to some people) beautiful. Because these stages mean that fungi can look very different, and often these fungi are not amenable to life in the laboratory (e.g. we can’t get it to complete the lifecycle in an petri dish in the lab), it was the case that observed asexual (or anamorphic) and sexual (teleomorphic) forms of a species get different names. For some species, connecting the two forms has eluded mycologists, and those which had a lack of a sexual stage were called Fungi Imperfecti. Some fungi are only thought to have an asexual stage, though that may change as more molecular and other data is developed.

If we don’t share names that refer to the same thing, how do I know the mushroom you found in Alaska is the same as the one from North Carolina?  Enter molecular identification of species by genotyping a common marker sequence such as the ITS spacer region of Fungi. The ITS region (Intergenic Internal Transcribed Spacer) has been proposed as the best molecule for this based on a variety of analyses and has been deployed in labs for many years. Other marker sequences (such as intron and COX1/COI) have been proposed but so far it appears that ITS is the blessed marker for fungi by the Barcode of Life project for the time being (see the fungal barcoding site too). The recent Amsterdam declaration proposed we could name fungi with a single name based on this marker sequence and perhaps simplify life for new students learning to memorize two names for a fungus which has a sexual and asexual lifecycle.

A summary of the history and challenges here can be found in a recent paper in IMA Fungus by John Taylor One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR (available pre-print here). In particular we can see that at least two papers have gone ahead and taken the Amsterdam proposal to heart and had already starting named one name for groups of fungi (perhaps predating the proposal) and removing what may seem confusing and perhaps outdated approach of teleomorph and anamorph naming. See Houbraken et al and also Crous et al where the authors state “Separate teleomorph and anamorph names are not provided for newly introduced genera, even where both morphs are known”.

Many mycologists are looking on as to what will happen next as to the naming of future species and how we unify this. We also hope to have better approaches to naming Environmental sequences which are only known by the sequence of ITS obtained from a soil, water, air, plant material sequencing experiment. A discussion held at the MSA meeting in Fairbanks will produce a more mature position paper lead by David Hibbett that can be discussed and vetted by the community as to how to proceed with deluge of new unidentified species that will emerge from large scale pyrosequencing of environments. If you have ideas, concerns, or want to read and comment on the current ideas in the proposal, please contact David. Hopefully we can surf this wave and get new names in the system lest we be swept away by it!

John W Taylor (2011). One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR IMA Fungus, 2 (2) : 10.5598/imafungus.2011.02.02.01

Houbraken, J., Frisvad, J., & Samson, R. (2010). Taxonomy of Penicillium citrinum and related species Fungal Diversity, 44 (1), 117-133 DOI: 10.1007/s13225-010-0047-z

Microsporidia genomes on the way

New genomes from Microsporidia are on the way from the Broad Institute and other groups, and will be a boon to those working on these fascinating creatures. Microsporidia are obligate intracellular parasites of eukaryotic cells and many can cause serious disease in humans. Some parasitize worms and insects too. The evolutionary placement of these species in the fungi is still debated with recent evidence placing them as derived members of the Mucormycotina based on shared synteny (conserved gene order), in particular around the mating type locus.  There is still some debate as to where this group belongs in the Fungal kingdom, with their highly derived characteristics and long branches they are still make them hard to place.  The synteny-based evidence was another way to find a phylogenetic placement for them but it would be helpful to have additional support in the form of additional shared derived characteristics that group Mucormycotina and Microsporidia. There is hope that increased number of genome sequences and phylogenomic approaches can help resolve the placement and more further understand the evolution of the group.

For data analysis, a new genome database for comparing these genomes is online called MicrosporidiaDB. This project has begun incorporating the available genomes and providing a data mining interface that extends from the EuPathDB project.

Early branching genomes available

Genome sequencing is underway on several early branches in the Opisthokont and some related linages as part of the “Origins of Multicellularity” project at the Broad Institute (BI) include some recently made available assemblies for:

  • Allomyces macrogynus (Blastocladiomycota “Chytrid”)
  • Capsaspora owczarzaki (Ichthyosporea)

Already available data from

Still in progress (BI)

Still in progress (Other centers)

Monophyly of Taphrinomycotina

A recent paper in MBE  presents evidence that the Taphrinomycota (containing S. pombe and Pneumocystis) are in fact a monophyletic group. This is considered an early branch in the Ascomycota with the Pezizomycotina (filamentous ascomycete fungi like Neurospora and Aspergillus) and Saccharomycotina (fungi mainly with yeast forms including Candida and Saccharomyces).  The monophyly of Taphrinomyoctina fungi is something that has been fairly accepted but there are a few publications reporting  conflicting evidence in some sets gene trees. This conflict is most likely due to Long Branch Attraction (LBA) and the Philippe lab has long worked on this problem of LBA working to develop tools like PhyloBayes that attempt to correct for LBA with a parameter rich model and using lots of data (like whole genomes).  These authors are employing phylogenomics in the sense that multiple genes are used to reconstruct the phylogeny.  This use is different from the J.Eisen/Sjölander sense which is to infer gene function from a phylogeny.

This paper presents evidence using proteins of 113 mitochondrial and nuclear genes and finds strong statistical support for this monophyly.  They also note that it was necessary to remove fast evolving sites from a dataset of only mitochondrial genes in order to overcome LBA artifacts that lead to Saccharomyces and S. pombe sister relationship in previous analyses.

This paper also presents work using the Pneumocystis genome sequence helps resolve its placement and eventually understanding the evolution of this pathogen.  In this tree the sister group to Pneumocystis is Schizosaccharomyces but both lineages have very long branches.  The Saitoella lineage is basal in this paper which is different from what was found with a 4 gene (AFTOL) dataset (see Figure 2). Further work sampling more genes from these Taphrina lineages will likely help resolve the intra-clade relationships.

Y. Liu, J. W. Leigh, H. Brinkmann, M. T. Cushion, N. Rodriguez-Ezpeleta, H. Philippe, B. F. Lang (2008). Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts Molecular Biology and Evolution, 26 (1), 27-34 DOI: 10.1093/molbev/msn221

A lot can happen after a few drinks: Saccharomyces hybridization

We may have to reevaluate whether Saccharomyces cerevisiae alone is the species used to brew beer.  A paper from Gonzalez et al describes results from PCRRFLP comparison of 24 brewing strains identifies evidence for S. cerevisiae x S. kudriavzevii hybrids.  Although this hybridization is not unprecedented, most seem to be related to cultivated brewing or fermentation strains.  It seems that the hybrids are better able to cope with the stress associated with fermentation process.

Sacch tree

It seems these would also be a great test system for more whole genome sequencing or at least more polymorphism comparisons to try and determine the proportion of the genome that comes from different parents and estimate timing and frequency of hybridization.  It seems possible that the hybridizations are occurring multiple times in nature so are the same regions from each parental genome kept in the hybrid offspring that are selected for fitness under fermentation stress?

Gonzalez, S.S., Barrio, E., Querol, A. (2008). Molecular Characterization of New Natural Hybrids of Saccharomyces cerevisiae and S. kudriavzevii in Brewing . Applied and Environmental Microbiology, 74(8), 2314-2320. DOI: 10.1128/AEM.01867-07

Cryptococcus species deliniation What delineates species boundaries in fungi? Much work has been done on biological and phylogenetic species concepts in fungi. Some concepts are reviewed in Taylor et al 2006 and in Taylor et al 2000, and applications can be seen in several pathogens such as Paraccocidiodies, Coccidioides, and the model filamentous (non-pathogenic) fungus Neurospora.

A paper in Fungal Genetics and Biology on species definitions in Cryptococcus neoformans from multi-locus sequencing seeks to provide additional treatment of the observed diversity. A large study of 117 Cryptococcus isolates were examined through multi-locus sequencing (6 loci) and identified two monophyletic lineages within C. neoformans varieties that correspond to var. neoformans and var. grubii. However within the C. gattii samples they identified four monophyletic groups consistent with deep divergences observed from whole genome trees for two strains of C. gattii, MLST, and AFLP studies. By first defining species, we can now test whether any of the species groups have different traits including prevalence in clinical settings and in nature.

BOVERS, M., HAGEN, F., KURAMAE, E., BOEKHOUT, T. (2007). Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing. Fungal Genetics and Biology DOI: 10.1016/j.fgb.2007.12.004

Phytopathogenic Fungi: what have we learned from genome sequences?

ResearchBlogging.orgA 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.

They infer from phylogenies we’ve published (Fitzpatrick et al, James et al) that plant pathogenic capabilities have arisen at least 5 times in the fungi and at least 7 times in the eukaryotes. In addition they use data on gene duplication and loss in the ascomycete fungi (Wapinski et al) to infer there large numbers of losses and gains of genes have occurred in fungal lineages.

Continue reading Phytopathogenic Fungi: what have we learned from genome sequences?

ISMB/ECCB 2007 recap

ISMB2007Back from ISMB/ECCB and a mountain of things left undone that somehow still need doing … including a quick entry about what was interesting at the conference.

I heard many good talks and only a few bad ones – maybe I guessed properly in darting between the multiple sessions. The meeting itsself was much better than past ones I had attended. The combination of Special Interest Groups meeting (BOSC, AFP, and Microbial Comparative Genomics being the ones I spent my time in). I got to give my talks and tutorial during the first few days and was able to just try and soak up the rest of the meeting (when my brain wasn’t melting from the heat). Particularly good was Carole Goble’s presentation on 7-deadly sins of bioinformatics software development.

Some general evolutionary talks that I found really interesting (some of these are probably biased since I count many of the presenters as friends):

I’ll write a quick post on the BoF session on open source and data sharing as well.

Todd and I took some pictures as well.

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.