title: A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim.
abstract: The Justinianic Plague, which started in the sixth century and lasted to the mid eighth century, is thought to be the first of three historically documented plague pandemics causing massive casualties. Historical accounts and molecular data suggest the bacterium Yersinia pestis as its etiological agent. Here we present a new high-coverage (17.9-fold) Y. pestis genome obtained from a sixth-century skeleton recovered from a southern German burial site close to Munich. The reconstructed genome enabled the detection of 30 unique substitutions as well as structural differences that have not been previously described. We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestis genome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth century in rural southern Germany.
authors: Max Planck Institute for the Science of Human History, Jena, Germany.|Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
authors: Michal
authors: M
authors: Feldman
authors: SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany.
authors: Michaela
authors: M
authors: Harbeck
authors: Max Planck Institute for the Science of Human History, Jena, Germany.|SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany.
authors: Marcel
authors: M
authors: Keller
authors: Max Planck Institute for the Science of Human History, Jena, Germany.|Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
authors: Maria A
authors: MA
authors: Spyrou
authors: SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany.
authors: Andreas
authors: A
authors: Rott
authors: SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany.
authors: Bernd
authors: B
authors: Trautmann
authors: Bundeswehr Institute of Microbiology, Munich, Germany.|German Center for Infection Research (DZIF), Munich, Germany.
authors: Holger C
authors: HC
authors: Scholz
authors: Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilian University Munich, Germany.
authors: Bernd
authors: B
authors: Päffgen
authors: SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany.|Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University of Munich, Germany.
authors: Joris
authors: J
authors: Peters
authors: Department of History, Harvard University, Initiative for the Science of the Human Past.
authors: Michael
authors: M
authors: McCormick
authors: Max Planck Institute for the Science of Human History, Jena, Germany.|Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
authors: Kirsten
authors: K
authors: Bos
authors: Max Planck Institute for the Science of Human History, Jena, Germany.|Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
authors: Alexander
authors: A
authors: Herbig
authors: Max Planck Institute for the Science of Human History, Jena, Germany.|Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
authors: Johannes
authors: J
authors: Krause
mesh_terms: D001483:Base Sequence; D000072441:DNA, Ancient / Q000032:analysis*; D004269:DNA, Bacterial / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D058873:Pandemics; D010930:Plague / Q000382:microbiology*; D014774:Virulence / Q000235:genetics; D015010:Yersinia pestis / Q000235:genetics*
chemical_list: D000072441:DNA, Ancient; D004269:DNA, Bacterial
keywords: Yersinia pestis; ancient DNA; justinianic plague; reconstruction; whole genome