Genome halving

Abstract

Genome duplication is an important source of new gene functions and novel physiological pathways. In the course of evolution, the nucleotide sequences of duplicated genes tend to diverge through mutation, so that one copy loses function (becomes a pseudogene) or develops a new function, encoding a distinct but similar product. Originally a duplicated genome contains two identical copies of each chromosome, but through inversion or other intrachromosomal movement, the gene orders in each pair of chromosomes change independently, and through reciprocal translocation, parallel linkage patterns between the two copies are disrupted. Eventually, all that can be detected are several chromosome segments of greater or lesser length (blocks), each of which appears twice in the genome, containing many paralogous genes in parallel orders. The study of genome duplication based on block data includes the inference of the synteny or linkage structure of the pre-duplication genome, the nature of the post-duplication rearrangement events, and the statistics of gene loss versus functional divergence. We propose a suite of Genome halving problems for algorithmic solution, some of which address the evolution of gene order, and others which deal with relations of synteny only. We present an efficient and accurate heuristic for the latter type of problem, and apply it to the genome duplication which has been described for Saccharomyces cerevisiae.