Tag Archives: phylogenomics

Postdoc: Comparative genomics and bioinformatics

Postdoc position in comparative genomics and bioinformatics

Applications are invited for a bioinformatics postdoctoral position in ?the research group of Laszlo G Nagy (Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary). We are now looking to hire new people with a background in bioinformatics, phylogenetics or fungal evolution. The Lab offers excellent training opportunities in fungal comparative genomics, cutting edge projects, abundant funding, an inspiring atmosphere and extensive collaborator network.

The primary focus of the lab is understanding the general principles of convergent evolution and fungal multicellularity through comparative genomics, transcriptomics and single-cell transcriptomics of multicellular fruiting bodies in Basidiomycetes. Fruiting bodies represent some of the most complex morphological structures found in fungi, yet, their developmental and evolutionary origins are hardly known. Complex fruiting bodies have evolved independently several times in the Basidiomycetes, offering an excellent model system to study the genetic mechanisms of convergent evolution.

The successful Candidate has:

  • PhD in bioinformatics, evolutionary biology, mycology or other relevant field
  • Experience in genomics, Perl and/or Python scripting
  • Good team player traits
  • Experience in working with fungi is a plus

Contact and application – The starting date of the project is September 2015. The position will last for one year with the possibility of extension up to 4 years. If interested, send a motivation letter along with your CV to Laszlo Nagy (lnagy@brc.hu).

Dr. Laszlo Nagy
Fungal Evolution & Genomics Lab
Synthetic and Systems Biology Unit, Institute of Biochemistry
Biological Research Center, HAS


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

Fungal P450s

A paper (Park et al, BMC Genomics) from Fungal Bioinformatics Lab at Seoul University in South Korea describes their new “Fungal P450 Database”. The database contains sequence, names, and genome links for P450’s (or Cytochrome P450s) identified by similarity and phylogenetic classification from genome annotations.  The group is using most of annotated genomes in GenBank (and I think some from elsewhere) of bacterial, fungi, animals, and plants.

I find the current nomenclature for this family of genes confusing but it has been I am sure a difficult job and wrangled to a large part by David Nelson (who also has a new paper on the CYPome of Aspergillus nidulans). I have found it difficult to follow the logic for naming these members, as it didn’t seem to be particularly phylogenetic at first, although I think that has improved. However, a stable and solid reference database is needed to for naming these gene members and for mapping new members in through straightforward analyses is an essential resource. Park et al have made great inroads to that end and it may indeed meet needs (I am cautious to say it is solved without more exploration or some sense of whether it is intended or will be taken up as just that sort of reference by the P450 community).  It has seemed to me that a proper phylogenetic (or really, a phylogenomic) approach is essential for naming the P450 member genes as orthologous or paralogous members across multiple species. The group has defined their classes as clusters of homologs (e.g. Mg004 is Magnaporthe grisea gene in Cluster 9.1) and linked these also to the Nelson nomeclature (CYP68E1).  By defining orthologous family members we can make more interpretations about how to transfer functional annotation in a truly phylogenomic context. 

The overall family is so large and diverse (they report 4538 fungal P450s into 141 clusters/sub-families from 68 species) across many different species. The fungi tend to have very large families in some clades (e.g. some filamentous fungi) so I think this type of systematic and searchable system that will have stable identities for clusters is an essential resource. I know I’m going to try and give it a whirl. We have a couple of cool findings about changes in the P450 families in Basidiomycete Coprinopsis and related species comparisons that I hope we’ll be able to better interpret with this additional phylogenomic naming of gene family members.

Jongsun Park, Seungmin Lee, Jaeyoung Choi, Kyohun Ahn, Bongsoo Park, Jaejin Park, Seogchan Kang, Yong-Hwan Lee (2008). Fungal cytochrome P450 database BMC Genomics, 9 (1) DOI: 10.1186/1471-2164-9-402