Improved assemblies and comparison of two ancient Yersinia pestis genomes

Yersinia pestis is the causative agent of the bubonic plague, a disease responsible for 9 several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible 10 the sequencing of whole genomes of important human pathogens, including the ancient Yersinia pestis 11 strains responsible for important outbreaks of the bubonic plague in London in the 14th century and 12 in Marseille in the 18th century among others. However, aDNA sequencing data are still characterized 13 by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging 14 and prevents in many cases a detailed study of genome rearrangements. It has recently been shown 15 that comparative sca↵olding approaches can improve the assembly of ancient Yersinia pestis genomes 16 at a chromosome level. In the present work, we address the last step of genome assembly, the gap17 filling stage. We describe an optimization-based method AGapEs (Ancestral Gap Estimation) to fill in 18 inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA 19 reads. We show how this approach can be used to refine comparative sca↵olding by selecting contig 20 adjacencies supported by a mix of unassembled aDNA reads and evolutionary parsimony signal. We 21 apply our method to two ancient Yersinia pestis genomes from the London and Marseilles outbreaks 22 of the bubonic plague. We obtain highly improved genome assemblies for both the London strain and 23 Marseille strain genomes, comprised of respectively five and six sca↵olds, with 95% of the assemblies 24 supported by ancient reads. We analyze the genome evolution between both ancient genomes in terms 25 of genome rearrangements, and observe a high level of synteny conservation between these two strains. 26