The inference of genome rearrangement requires detailed gene maps of related species. For most multichromosomal species, however, knowledge of chromosomal assignment of genes outstrips mapping data. Comparison of these species is thus a question of comparing sets of syntenic genes, without any gene order or gene orientation information. Given synteny data from present-day species, can we infer the synteny sets of ancestor species? How many chromosomes did these ancestors possess, and what genes were on each one? We first study the problem of calculating a syntenic edit distance between two genomes, based on reciprocal translocation, chromosome fusion and fission. This distance is then used in the analysis of the median problem for synteny, and hence for a prelimary approach to phylogenetic inference of synteny.
KeywordsGenome Rearrangement Phylogenetic Inference Reciprocal Translocation Internal Vertex Terminal Vertex
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- 1.S. Hannenhalli and P.A. Pevzner. Transforming cabbage into turnip. (polynomial algorithm for sorting signed permutations by reversals). Proceedings of the 36th Annual Symposium on Foundations of Computer Science, 1995.Google Scholar
- 2.J. Kececioglu and D. Sankoff. Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement. Algorithmica, 13:180–210, 1995.Google Scholar
- 4.D. Sankoff, G. Leduc, N. Antoine, B. Paquin, B.F. Lang, and R. Cedergren. Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proceedings of the National Academy of Sciences USA 89, 6575–6579, 1992.Google Scholar
- 5.I. A. Zakharov. Measurements of similarity of synteny groups and an analysis of genome rearrangements in the evolution of mammals. In Bioinformatics, supercomputing and complex genome analysis, H. Lim, J. Fickett and C. Cantor (eds), World Scientific, 1993.Google Scholar
- 6.B. Das Gupta, T. Jiang, S. Kannan, M. Li, and Z. Sweedyk. Personal communication, March 1996.Google Scholar