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There are several databases that include orthology prediction for fungi. These all have pros and cons. Some are more comprehensive and have many more species. Some are curated orthologies and paralogy which should be pretty stable. Some are automated and groupings and ortholog group IDs change at each iteration. A phylogenetic approach from a Saccharomyces perspective is [...] Gene sequences evolve at different rates due to different constraints, either due to chromosome position, functional constraint, and status as a single-copy or multi-copy gene. In a recent paper, Allen Rodrigo (the new NESCent director by the, way, congrats!) the authors hypothesize that correlation in branch lengths of gene trees suggest they operate in the same [...] Take a look at this post by Larry Moran on Takao Kasuga’s paper on phylogenetic distribution of genes in N. crassa genome. [...] 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). [...] |
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