title: 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.
authors: Laboratory of Computational Biology and Bioinformatics, EPFL, 1015 Lausanne, Switzerland. yann.christinat@epfl.ch
authors: Yann
authors: Y
authors: Christinat
authors: Bernard M E
authors: BM
authors: Moret
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D000818:Animals; D019143:Evolution, Molecular; D005091:Exons; D005136:Eye Proteins / Q000235:genetics; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D007438:Introns; D008957:Models, Genetic; D018992:Myelin-Associated Glycoprotein / Q000235:genetics; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors / Q000235:genetics; D010802:Phylogeny; D012097:Repressor Proteins / Q000235:genetics
chemical_list: D005136:Eye Proteins; D018398:Homeodomain Proteins; D018992:Myelin-Associated Glycoprotein; D000071841:PAX6 Transcription Factor; C000605730:PAX6 protein, human; D051761:Paired Box Transcription Factors; D012097:Repressor Proteins