This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison
LDLR Gene Phylogeny
Gene phylogeny was analyzed with phylogeny.fr using the mRNA sequences of all homologous genes identified on Homologene. The MUSCLE algorithm was used, along with TreeDyn in order to create the evolutionary tree. The ClustalW algorithm could not be used because the mRNA average sequence was too long. TreeFam was utilized in order to visualize a tree containing paralogs of the LDLR gene.
Figure 1-MUSCLE algorithm tree
The evolutionary lineage given in the tree follows the sequence homology determined by BLAST. As expected, Pan troglodytes is the closest relative to Homo sapiens, while Danio rerio is the most divergent of the homologous genes.
TreeFam gave a large tree containing 153 genes related to Homo sapiens LDLR. VLDLR (very low density lipoprotein receptor) and LRP8 (low density lipoprotein receptor-related protein 8) are shown to be paralogs to LDLR, and interestingly, this tree identified Canis familiarasas as having an ortholog to LDLR. TreeFam further demonstrates the deep evolutionary conservation of LDLR and related genes. Because of the size of this tree it can be viewed here.
