An upgrade and revision of the chimpanzee reference genome

Abstract

Comparative and evolutionary genomics currently highly rely on genome reference assemblies in order to detect variation between different organisms or species. However, the vast majority of current assemblies are based on whole genome shotgun (WGS) sequencing, a technique known to systematically underrepresent certain complex, and potentially biologically relevant, regions of the genome. Furthermore, these assemblies are highly fragmented in terms of contig and scaffold continuity, leading to fragmented or fully missing gene models and a general loss of information. The genome of our closest living evolutionary relative, the chimpanzee, is of key importance to study the evolutionary trajectories of our own species. Nevertheless, its current reference assembly is also based on a WGS and therefore only a draft and a highly fragmented representation of the genome with still over 25,000 scaffolds and 100,000 gaps. Here, we will present our efforts to apply and integrate different 3rd generation sequencing technologies as well as novel genome assembly strategies to resolve most of the complex and missing sequences of the current chimpanzee genome reference, trying to bring its quality closer to the human reference.