Inferring transcript phylogenies

Abstract

Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals--some researchers conjecture that up to 90% of human genes are alternatively spliced. Despite much research on exon and intron evolution, little is known about the evolution of transcripts.In this paper, we present a model of transcript evolution and an associated algorithm to reconstruct transcript phylogenies. The evolution of the gene structure--exons and introns--is used as basis for the reconstruction of transcript phylogenies. We apply our model and reconstruction algorithm on two well-studied genes, MAG and PAX6, obtaining results consistent with current knowledge and thereby providing evidence that a phylogenetic analysis of transcripts is feasible and likely to be informative.

Transcripts’ Evolutionary History and Structural Dynamics Give Mechanistic Insights into the Functional Diversity of the JNK Family

“…1a), and the exon usage of a transcript can change along the branches upon the inclusion or exclusion of one or several exons (which we refer to as "mutations"). The underlying evolutionary model is comprised of two levels, following 16 . At the level of the gene, exons can be absent, constitutive, or alternative (i.e.…”

“…PhyloSofS algorithm seeks to determine the scenario with the smallest number of evolutionary events, following the maximum parsimony principle. It is inspired from that reported in 16 . Our main contribution was to develop heuristics in order to treat complex cases in a computationally tractable way.…”

“…We model transcripts evolution as a two-level process, at the gene and transcript levels, as described by Christinat and Moret 16 . At the level of the gene, each exon can be either absent, alternative or constitutive.…”

“…As in 16 , the g s vectors for internal nodes (ancestral species) are determined by using Sankoff's algorithm 62 . Dollo's parsimony principle is also respected, such that an exon cannot be created twice 2 .…”

“…We should stress that PhyloSofS algorithm is designed to deal with much more complex cases than those reported in 16 PhyloSofS generates PDF files displaying the computed transcripts' phylogenies using a Python driver to the Graphviz 23 DOT format.…”