Abstract
The popularization of sequencing technologies in the past twenty years led to a high increase of the number of sequenced genomes. The diversity of the newly sequenced reference genomes highlighted the biases of using a single reference, which is not enough to access all the diversity within a species. There are many examples of intraspecific variations within plants, including presence / absence and copy number variations. These variations can have a strong effect on plant phenotypes, as exemplified by the African rice in which the presence of the gene Sub1A is linked to drought tolerance. The concept of pangenome appeared to better integrate these variations within genomics approaches. A pangenome can be built from genes only or from any genomic fragments found within a group, and is useful to compare their distributions between multiple individuals. Depending on the presence rate, many categories of elements can be defined; the main ones are the elements present in all the individuals (part of the ‘core’ genome) and these absent in at least one of them (part of the ‘variable’ genome). Pangenomics still lacks tools, especially for visualization. This is particularly true for eukaryotes (including plants) which have larger and more complex genomes than bacteria. Pangenomes were first built for bacteria, but their related tools cannot properly work on bigger genomes. My PhD investigated the creation of novel visual representations and tools for the visualization of plant pangenomes (and eukaryotes in general).Within this dissertation, I introduce the state of the art of pangenome visualization: I distinguish pan-gene from pangenomes, the latter often being represented by pangenome graphs where each sequence is a node and each observed sequence succession forms an edge; I also identify unspecific, qualifying, positioned, structural and composite visualization tools. The first chapter introduce ten principles for creating a genomic visualization tool, for future biology or bioinformatics scientists interested in datavisualization. The second chapter describes my first pangenome visualization, published in the journal Bioinformatics under the name ‘Panache: a Web Browser-Based Viewer for Linearized Pangenomes’. I detail the visual representation used within Panache and the creation of the resulting web application built in JavaScript, enabling the dynamic exploration of pangenomic data. The third and final chapter details the design of a composite visualization tools for pangenomes, called SaVanache, and enabling the navigation between four view scales. There are four of them: one for global diversity, one for structural variations, one for the presence / absence variations, and one for nucleotide variations. I propose a new approach for the annotation and visual representation of structural variations within a pangenome graph, based on a pivot path within the graph used as a reference coordinate system.