Authors: Cade Mirchandani 1; Russell Corbett-Detig 1,2
Affiliations: 1) Department of Biomolecular Engineering, University of California Santa Cruz. Santa Cruz, CA 95064, USA; 2) Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Keywords: Comparative genomics & genome evolution
Although linear reference genomes are a powerful resource for population and evolutionary genomics, each represents only a fraction of the diversity in most natural populations. The Drosophila Genome Nexus is a population genomics resource composed of high quality D. melanogaster genome assemblies from many different geographic regions. However, comparative analysis of Drosophila genomes are constrained by the use of a single reference genome. Here, we present a significant improvement to the resource by integrating all of the genomes from the DGN into a reference pangenome graph. We align all previous DGN genomes, along with newly published genomes to the reference genome graph using a singular workflow to allow comparison across datasets. Using our reference genome graph, we observe significantly increased alignment sensitivity when compared to mapping to a linear reference genome. Furthermore, we show that genotype calls for highly variable isolates are unbiased when aligned to the pangenome graph. The addition of the reference genome graph to this resource will allow users to leverage known wild variation in alignments and downstream analysis of their own data. These improvements to this resource will help address the broad range of population genetic questions in D. melanogaster and provide a roadmap for improving variant calls in other highly variable genomes.