Marta Farré-Belmonte: Tracing chromosome rearrangements in mammals

Chromosome rearrangements are a hallmark of genome evolution and essential for understanding the mechanisms of speciation and adaptation. Determining chromosome rearrangements over evolutionary time scales has been a difficult problem, primarily because of the lack of high-quality, chromosome-scale genome assemblies that are necessary for reliable reconstruction of ancestral genomes. For closely related species with good map-anchored assemblies, such as human, chimpanzee, and rhesus, it is possible to infer most inversions, translocations, fusions, and fissions that occurred during evolution by simple observational comparisons. However, for sequence-based genome-wide comparisons that require resolving large numbers of rearrangements of varying scale, determining ancestral chromosomal states is challenging both methodologically and computationally because of the complexity of genomic events that have led to extant genome organizations, including duplications, deletions, and reuse of evolutionary breakpoint regions flanking regions of homologous synteny. In this seminar I will present recent tools developed by my group to define chromosome rearrangements from the ancestor of all mammals. Then I will focus on the application of these tools in two mammalian clades (ruminants and rodents) where we are combining transcriptomics and epigenomics data to understand the possible role of chromosome rearrangements.