Multi-Break Rearrangements and Breakpoint Re-Uses: From Circular to Linear Genomes

Abstract

Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2-break rearrangements represent standard reversals, fusions, fissions, and translocations, 3-break rearrangements represent a natural generalization of transpositions. Pevzner (2007a, 2008a) studied multi-break rearrangements in circular genomes and further applied them to the analysis of chromosomal evolution in mammalian genomes. In this paper, we extend these results to the more difficult case of linear genomes. In particular, we give lower bounds for the rearrangement distance between linear genomes and for the breakpoint re-use rate as functions of the number and proportion of transpositions. We further use these results to analyze comparative genomic architecture of mammalian genomes.

Anchoring the dog to its relatives reveals new evolutionary breakpoints across 11 species of the Canidae and provides new clues for the role of B chromosomes

“…In a similar manner, cytogenetic evaluation has been crucial to understanding the complex chromosome changes that occur in cancer and congenital abnormalities. The fragile breakage model (FBM) was developed to explain the identification of shared chromosome breakpoints, evident in evolution and diseased karyotypes, especially mammalian cancers (Pevzner and Tesler 2003;Murphy et al 2005;Peng et al 2006;Alekseyev andPevzner 2007, 2010;Alekseyev 2008).…”

Linearization of Median Genomes under DCJ

“…Below we briefly describe the concepts of genome graphs and DCJs (2-breaks), for further details we refer the reader to [9,17].…”

“…solution to L-GMP, the DCJ distance gives a good approximation for genomic distance [17] and simplifies the genome rearrangements analysis. As soon as the genome M is constructed, its transformations into the given genomes (or vice versa) with genome rearrangements (preserving linearity along all intermediate genomes) can be obtained with GRIMM [18].…”

Breakpoint graphs and ancestral genome reconstructions

“…However, rearrangement scenarios in linear genomes are well approximated by 2-break scenarios in circular genomes (Alekseyev 2008). Hence, we use 2-breaks as a single substitute for reversals, translocations, fusions, and fissions, admitting that 2-breaks may violate linearity of the genomes by creating circular chromosomes.…”