Algorithms for Molecular Biology 11.1 Genome Rearrangements 11.1.1 Preface 11.1.2 Operations on Chromosomes

It has been a well known fact for over 60 years that the genome undergoes rearrangements, or what seem to be a general scrambling of the order of the genome. In the salivary glands of Drosophila, a phenomenon of chromosomes doubling in thickness during mitosis has been noticed. This appears to be two homologs (identical copies of a chromosome segment created during cell division) that have glued together somehow. The chromosomes have an observable pattern of bands perpendicular to their length, which were studies since the 1920's. This pattern is characteristic of a species. However, at times one can nd two individuals of the species who show diierent patterns of these bands; usually the diierences appear to be segment reversals along the pattern of bands. What kinds of genome rearrangement events (also called operations) take place? 1. Operations on a single chromosome: Deletions (a certain part is lost, for example abc ! ac) Insertions (a part is added, for example ac ! abc) Duplications (can be tandem, for example abc ! abbc, or not, for example abc ! abcb) Reversals, or inversions (a part is turned around, head to tail, for example abc 1 c 2 c 3 c 4 de ! abc 4 c 3 c 2 c 1 de) Transpositions (two parts change places, for example abcd ! acbd) How do these operations take place? If two areas in a chromosome have a pretty high homology, they might attach just like two diierent strands of the double helix. Once they are attached, a loop forms. This loop might be discarded (deletion), or switched (inversions).