Sorting genomes by prefix double-cut-and-joins

In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double- cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and recombine the severed endpoints in one of two possible ways: one of these options corresponds to a prefix reversal, which reverses the order of elements between the two cuts (as well as their signs in the signed case). Our main results are: (1) new structural lower bounds based on the breakpoint graph for sorting by unsigned prefix reversals, unsigned prefix DCJs, and signed prefix DCJs; (2) two polynomial-time algorithms for sorting by prefix DCJs, both in the signed case (which answers an open question of Labarre [1]) and in the unsigned case; (3) a 1-absolute approximation algorithm for sorting by unsigned prefix reversals for a specific class of permutations.