Early eukaryote evolution based on mitochondrial gene order breakpoints.
The comparison of the gene orders in a set of genomes can be used to infer their phylogenetic relationships and to reconstruct ancestral gene orders. For three genomes this is done by solving the "median problem for breakpoints"; this solution can then be incorporated into a routine for estimating optimal gene orders for all the ancestral genomes in a fixed phylogeny. For the difficult (and most prevalent) case where the genomes contain partially different sets of genes, we present a general heuristic for the median problem for induced breakpoints. A fixed-phylogeny optimization based on this is applied in a phylogenetic study of a set of completely sequenced protist mitochondrial genomes, confirming some of the recent sequence-based groupings which have been proposed and, conversely, confirming the usefulness of the breakpoint method as a phylogenetic tool even for small genomes.
Sankoff
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D
Centre de recherches mathématiques, Université de Montréal, Québec. sankoff@crm.umontreal.ca
Bryant
D
D
Deneault
M
M
Lang
B F
BF
Burger
G
G
D005075:Biological Evolution; D019295:Computational Biology; D004272:DNA, Mitochondrial / Q000235:genetics*; D005057:Eukaryotic Cells; D008957:Models, Genetic; D010802:Phylogeny
D004272:DNA, Mitochondrial