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 pathway or have a similar function. To do this they took alignments of orthologous genes from 10 bacterial species which were seeded with E. coli as the target species. The alignments were used to build trees with MrBayes and only those which recovered the known species topology were retained. The ortholog groups were assigned GO terms via similarities.
They then looked at the branch lengths of gene trees and found a correlation between GO categories and rates of gene evolution/shape of the tree. I’ll not go into more details here but I think this is an interesting finding that is probably not so surprising when you think about it. I’m be very curious to see if this held up much in multi-domained proteins as well and of course taking this approach for a drive in fungal orthologs would be an interesting project for someone to try.
Li WL, & Rodrigo AG (2009). Covariation of branch lengths in phylogenies of functionally related genes. PloS one, 4 (12) e8487. PMID: 20041191. doi:10.1371/journal.pone.0008487
I’ve been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.
Schmitt, I., Partida-Martinez, L.P., Winkler, R., Voigt, K., Einax, E., DÃ¶lz, F., Telle, S., WÃ¶stemeyer, J., Hertweck, C. (2008). Evolution of host resistance in a toxin-producing bacterialâ€“fungal alliance. The ISME Journal DOI: 10.1038/ismej.2008.19
LEVASSEUR, A. (2008). FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genetics and Biology DOI: 10.1016/j.fgb.2008.01.004
Shivaji, S., Bhadra, B., Rao, R.S., Pradhan, S. (2008). Rhodotorula himalayensis sp. nov., a novel psychrophilic yeast isolated from Roopkund Lake of the Himalayan mountain ranges, India. Extremophiles DOI: 10.1007/s00792-008-0144-z
Few organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise. What is curious is the large number of yeast genes for which we’ve been unable to characterize. Of the ~6000 genes currently identified in the yeast genome, 1253 have no verified function (for the uninclined, this is roughly 21% of the yeast proteome). Egads! If we can’t figure this out in yeast, what hope do we have in non-model organisms?Lourdes Peña-Castillo and Timothy R. Hughes discuss this curious observation and its cause in their report in Genetics.
Continue reading Yes, Ecology can improve Genomics
Ignazio 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