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Mane, Aniket - Genome rearrangement problems accounting for duplicate genes

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This thesis has been submitted to the Library for purposes of graduation, but needs to be audited for technical details related to publication in order to be approved for inclusion in the Library collection.

Term : Summer 2018

Degree : M.Sc.

Degree type : Thesis

Department : Department of Mathematics

Faculty : Science

Senior supervisor : Cedric Chauve

Thesis title : Genome rearrangement problems accounting for duplicate genes

Given names : Aniket

Surname : Mane

Abstract : We investigate certain genome rearrangement problems studied in relation to genome evolution. We introduce the SCJ-TD-FD rearrangement model to explain the directed evolution from an ancestor A to a descendant D, where D may contain multiple copies of genes from A. We study the pairwise genome distance problem that aims at finding the most parsimonious sequence of cuts, joins and single-gene duplications that transforms A to D, under this model. Next, we study the rooted median problem under the SCJ-TD-FD model, for which the problem is shown to be NP-hard. We provide an Integer Linear Program that, on simulated data, predicts an optimal median with high accuracy. Finally, we study the Small Parsimony Problem under the SCJ-TD-FD model that aims at finding the gene orders at the internal nodes of a given species tree. We define an ILP-based approach to reconstruct the ancestral gene orders and present our experiments on a data-set of Anopheles mosquito genomes.

Keywords : genome rearrangements, duplications, Single-Cut-or-Join, distance, parsimony, median

Total pages : 86