Pangenomics for Eukaryotes

Large-scale sequencing projects cause an increase in the number of available genome sequences and genomic data sets. Many plants and animals are therefore no longer represented by a single reference genome, but by a set of related genomes. This development asks for a shift from reference-centered analyses to pangenome analyses. Here we address the question: how can we condense multiple annotated genomes for a (group of) species in a single representation, which can be used to study genome variation and evolution? We have developed an algorithm to transform multiple sequences into a compressed de Bruijn graph and to store this highly connected data in a graph database. Genome annotation is added to the sequence graph, and even relationships between annotated features (such as orthology) can be included. The indexed graph representation can be queried and traversed to address biological questions, and our approach is scalable to large eukaryotic genomes. Methods for read mapping, structural variation detection, and visualization are under development. We believe a computational pangenome approach is essential if we want to study and exploit the genomic diversity in plant and animal genomes.