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The Design, Implementation and Application of a Computational Pipeline for the Reconstruction of the Gene Order on the Chromosomes of Very Ancient Ancestral Species

This thesis presents a novel approach to reconstructing ancestral genomes of a number of descendant species related by a phylogeny. Traditional methods face challenges due to cycles of whole genome doubling followed by fractionation in plant lineages. In response, the thesis proposes a new approach that first accumulates a large number of candidate gene adjacencies specific to each ancestor in a phylogeny. A subset of these which to produces long ancestral contigs are chosen through maximum weight matching. The strategy results in more complete reconstructions than existing methods, and a number of quality measures are deployed to assess the results.
The thesis also presents a new computational technique for estimating the ancestral monoploid number of chromosomes, involving a "g-mer" analysis to resolve a bias due to long contigs and gap statistics to estimate the number. The method is applied to a set of phylogenetically related descendant species, and the monoploid number is found to be 9 for all rosid and asterid orders. Additionally, the thesis demonstrates that this result is not an artifact of the method, by deriving a monoploid number of approximately 20 for the metazoan ancestor.
The reconstructed ancestral genomes are functionally annotated and visualized through painting ancestral projections on descendant genomes and highlighting syntenic ancestor-descendant relationships. The proposed method is applied to genomes drawn from a broad range of plant orders. The Raccroche pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree, and constructs chromosomes by counting the frequencies of ancestral contig co-occurrence on the extant genomes, clustering these for each ancestor, and ordering them.
Overall, this thesis presents a significant contribution to the field of ancestral genome reconstruction, offering a new approach that produces more complete reconstructions and provides valuable insights into the evolutionary process giving rise to the gene content and order of extant genomes.

Identiferoai:union.ndltd.org:uottawa.ca/oai:ruor.uottawa.ca:10393/45409
Date11 September 2023
CreatorsXu, Qiaoji
ContributorsSankoff, David
PublisherUniversité d'Ottawa / University of Ottawa
Source SetsUniversité d’Ottawa
LanguageEnglish
Detected LanguageEnglish
TypeThesis
Formatapplication/pdf

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