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

New species of Cryptococcus found in seawater

A paper in IJSEM describes a new species in the Cryptococcus basidiomycete yeast lineage. The name is proposed as Cryptococcus keelungensis sp. nov. for a strain isolated from the sea surface microlayer. Its identity as a Cryptococcus sp was determined by sequencing of 26S rDNA D1/D2 and ITS loci and molecular phylogenetics. This is quite diverged from the human pathogen Cryptococcus neoformans and C. gattii as the new species falls in the order Filobasidiales while C. neoformans is classified in the order Tremellales. Interestingly, based on the phylogeny in the paper it seems to be relatively close to newly discovered Cryptococcus himalayensis.

See also:

C.-F. Chang, C.-F. Lee, S.-M. Liu (2008). Cryptococcus keelungensis sp. nov., an anamorphic basidiomycetous yeast isolated from the sea-surface microlayer of the north-east coast of Taiwan INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 58 (12), 2973-2976 DOI: 10.1099/ijs.0.65773-0

Updated Cryptococcus serotype A annotation

SEM of clamp cell, yeast cells and sexual spore chains. Courtesy R. Velagapudi & J. Heitman

A new and improved annotation of Cryptococcus neoformans var grubii strain H99 (serotype A) has been made available in GenBank and the Broad Institute website. This update is collaboration between several groups providing data and analyses and the genome annotation team at the Broad Institute.

Some changes noted by the Broad Institute include:

“This release of gene predictions for the serotype A isolate Cryptococcus neoformans var. grubii H99 is based on a new genomic assembly provided by Dr. Fred Dietrich at the Duke Center for Genome Technology. The new assembly consists of 14 nuclear chromosomes and a single 21 KB mitochondrial chromosome, and has resulted in a reduction of the estimated genome size from 19.5 to 18.9 Mb. Improvements in the assembly and in our annotation process have resulted in a set of 6,967 predicted protein products, 335 fewer than the previous release.”

How to get A. fumigatus in the mood for love 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

Odds and ends