Genome rearrangements with duplications

Comparing genomes with rearrangements and segmental duplications

MOTIVATION Large-scale evolutionary events such as genomic rearrange.ments and segmental duplications form an important part of the evolution of genomes and are widely studied from both biological and computational perspectives. A basic computational problem is to infer these events in the evolutionary history for given modern genomes, a task for which many algorithms have been proposed under v...

With Micronuclear Genome Rearrangements

The micronuclear genome of Tetrahymena thermophila contains Tel-1 elements that structurally resemble transposons. Here we present molecular evidence that Tel-1 transposon-like elements are mobile. The arrangements of Tel-1 elements in the micronuclear genomes of several T. thermophila strains and cell lines were assayed by Southern blotting. The molecular evidence for Tel-1 transposition is mo...

Timing of Whole Genome Duplications

Segmental duplications mediate novel, clinically relevant chromosome rearrangements.

Copy number studies have led to an explosion in the discovery of new segmental duplication-mediated deletions and duplications. We have analyzed copy number changes in 2419 patients referred for clinical array comparative genomic hybridization studies. Twenty-three percent of the abnormal copy number changes we found are immediately flanked by segmental duplications > or =10 kb in size and > or...

Genome Rearrangements with Partially Ordered Chromosomes

Genomic maps often do not specify the order within some groups of two or more markers. The synthesis of a master map from several sources introduces additional order ambiguity due to markers missing from some sources. We represent each chromosome as a partial order, summarized by a directed acyclic graph (DAG), to account for poor resolution and of missing data. The genome rearrangement problem...