Reconstruction of Ancestral Gene Order after Segmental Duplication and Gene Loss

As gene order evolves through a variety of chromosomal rearrangements, conserved segments provide important insight into evolutionary relationships and functional roles of genes. However, gene loss within otherwise conserved segments, as typically occurs following large-scale genome duplication, has received limited algorithmic study. This has been a major impediment to comparative genomics in certain taxa, such as plants and fish. We propose a heuristic algorithm for the inference of ancestral gene order in a set of related genomes that have undergone large-scale duplication and gene loss. First, approximately conserved (i.e. homologous) segments are identified using pairwise local genome alignment. Second, homologous segments are iteratively clustered under the control of two parameters, (1) the minimal required number of shared genes between two clusters and (2) the maximal allowed number of rearrangement breakpoints along the lineage leading to each descendant segment. Finally, ...

• Type: Conference
• Year: 2003
• Where: CSB
• Authors: Jun Huan, Jan Prins, Wei Wang 0010, Todd J. Vision
• Keywords: Ancestral Gene Order, CSB 2003, Gene Loss, Gene Order