Gene Phylogenetic Trees

This web page was produced as an assignment for Gen677 at UW-Madison Spring 2009

GeneBee phylogenetic tree of SIRT6

 

This is a phylogenetic tree from GeneBee (1), this tree was constructed by comparing the DNA sequences for these seven different model organisms.   Demonstrated in this phylogenetic tree is that the human homology is very closely related to Pan troglodytes, seen  by the two branches being closer together.  The other not to surprising feature of this tree is that the mouse and rat are closely related and they are more closely related to humans. 

One possible down fall to this phylogenetic tree is source of the DNA sequences of  Gallus gallus, Mus musculus, Rattus norvegicus which are derived from mRNA and turned into cDNA so these contain sequences contain poly-A tail.  So the poly-A tail could lead to organism to seeming to have a more dissimilar sequence then is actually true.  So I did another sequence analysis this time I deleted the poly-A tail, but I obtained the same looking phylogenetic tree with only a high percent similarity of 37.4 compared to my other 37.  But I still have to wonder if these sequences would be more similar if they were DNA rather then mRNA. 

Other Phylogenetic tree

He is just another multiple sequence aliment of the DNA sequences that I found for SIRT6 by using phylogeny.fr website (2).  I see a exact replica of what I found for the GeneBee analysis.  So I think this demonstrates that the phylogenetic trees are very similar and that at least for SIRT6 the type of analysis does not make a difference as to how the phylogenetic tree is laid out.

Results of Phylogenetic tree

From my phylogenetic trees I am able to clearly see how each organisms SIRT6 is related to each other.  I found that SIRT6 in humans and Pan-troglodytes is the cloest relative to use.  While mouse and rat are similar to human SIRT6 but are more closly related to each other.  Its interesting to note that Gallus- Gallus is less related to human then rat or mouse.  And it wasnt to much of a supprise that Danio rerio and Drosophila are the furtherest in relatedness to humans.

References

 1. Brodsky, L.I., Ivanov, V.V., Kalaydzidis, Y.L., Leontovich, A.M., Nikolaev, V.K., Feranchuk, S.I., and Drachev, V.A.
     (1995). GeneBee-NET: Internet-based server for analyzing biopolymers structure. Biochemistry (Moscow),
     60(8):923-928. http://www.genebee.msu.su/services/papers/GNB-NET/GNB-NET.htm.

2. Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., Dufayard, J.F., Guindon, S., Lefort, V.,
     Lescot, M., Claverie, J.M., Gascuel, O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic
     Acids Research, 36(Web Server issue):W465-9. doi:10.1093/nar/gkn180

Mark Devries
Email [email protected]
last updated 1/22/09
http://www.gen677.weebly.com