Bioinformatický seminár

Tue 16 Oct. 2012, 17:20
I-9

Title: Olivier Tremblay Savard et al. Evolution of orthologous tandemly arrayed gene clusters
Speaker: Martin Kravec

BACKGROUND: Tandemly Arrayed Gene (TAG) clusters are groups of paralogous genes
that are found adjacent on a chromosome. TAGs represent an important repertoire
of genes in eukaryotes. In addition to tandem duplication events, TAG clusters
are affected during their evolution by other mechanisms, such as inversion and
deletion events, that affect the order and orientation of genes. The DILTAG
algorithm developed in 1 makes it possible to infer a set of optimal evolutionary
histories explaining the evolution of a single TAG cluster, from an ancestral
single gene, through tandem duplications (simple or multiple, direct or
inverted), deletions and inversion events. RESULTS: We present a general
methodology, which is an extension of DILTAG, for the study of the evolutionary
history of a set of orthologous TAG clusters in multiple species. In addition to 
the speciation events reflected by the phylogenetic tree of the considered
species, the evolutionary events that are taken into account are simple or
multiple tandem duplications, direct or inverted, simple or multiple deletions,
and inversions. We analysed the performance of our algorithm on simulated data
sets and we applied it to the protocadherin gene clusters of human, chimpanzee,
mouse and rat. CONCLUSIONS: Our results obtained on simulated data sets showed a 
good performance in inferring the total number and size distribution of
duplication events. A limitation of the algorithm is however in dealing with
multiple gene deletions, as the algorithm is highly exponential in this case, and
becomes quickly intractable.