Annotation of pangenome graphs

• Title: "Annotation of pangenome graphs" IRD.
  • PhD student: Nina Marthe.
  • Affiliated unit: IRD, UMR 233 - DIADE - Dynadiv.
  • Supervision:
    • François Sabot (IRD).
    • Doctoral school: Biodiversité, Agriculture, Alimentation, Environnement, Terre, Eau.
  • Project duration: 2023–2026.

Project summary:

Genomics seeks to elucidate the functioning of genomes to better understand life. Traditionally, it relies on the genome of a single individual, called the reference genome, which is used as a comparison point for the genetic data to be analyzed. However, the use of a reference genome has many limitations, particularly hindering the study of parts of the genome that are not present in all individuals and thus may be absent from the reference. These regions can contain many genes linked to species adaptation to their environment, making it important to consider them. The pangenome, which contains the genetic information of an entire population, is a promising tool to address this issue. To more easily exploit the information contained in pangenomes, my thesis will focus on their annotation, which involves locating the present genes and assigning them a function, thereby giving biological meaning to a DNA sequence.