a methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes相邻地区的方法论框架重建祖先基因组及其哺乳动物基因组中的应用.pdfVIP

A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes 1 2,3,4,5 Cedric Chauve , Eric Tannier * ˆ ´ ´ 1 Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada, 2 INRIA, Rhone-Alpes, France, 3 Universite de Lyon, Lyon, France, 4 Universite ´ ´ Lyon 1, Lyon, France, 5 Laboratoire de Biometrie et Biologie Evolutive, CNRS, UMR5558, Villeurbanne, France Abstract The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long- standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental