New ancient Eastern European  Yersinia pestis  genomes illuminate the dispersal of plague in Europe

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Yersinia pestis, the causative agent of plague, has been prevalent among humans for at least 5000 years, being accountable for several devastating epidemics in history, including the Black Death. Analyses of the genetic diversity of ancient strains of Y. pestis have shed light on the mechanisms of evolution and the spread of plague in Europe. However, many questions regarding the origins of the pathogen and its long persistence in Europe are still unresolved, especially during the late medieval time period. To address this, we present four newly assembled Y. pestis genomes from Eastern Europe (Poland and Southern Russia), dating from the fifteenth to eighteenth century AD. The analysis of polymorphisms in these genomes and their phylogenetic relationships with other ancient and modern Y. pestis strains may suggest several independent introductions of plague into Eastern Europe or its persistence in different reservoirs. Furthermore, with the reconstruction of a partial Y. pestis genome from rat skeletal remains found in a Polish ossuary, we were able to identify a potential animal reservoir in late medieval Europe. Overall, our results add new information concerning Y. pestis transmission and its evolutionary history in Eastern Europe.

This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

Related collections

Most cited references 49

Record: found
Abstract: found
Article: found

Is Open Access

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

Martin Kircher, Susanna Sawyer, Matthias Meyer (2011)

Due to the increasing throughput of current DNA sequencing instruments, sample multiplexing is necessary for making economical use of available sequencing capacities. A widely used multiplexing strategy for the Illumina Genome Analyzer utilizes sample-specific indexes, which are embedded in one of the library adapters. However, this and similar multiplex approaches come with a risk of sample misidentification. By introducing indexes into both library adapters (double indexing), we have developed a method that reveals the rate of sample misidentification within current multiplex sequencing experiments. With ~0.3% these rates are orders of magnitude higher than expected and may severely confound applications in cancer genomics and other fields requiring accurate detection of rare variants. We identified the occurrence of mixed clusters on the flow as the predominant source of error. The accuracy of sample identification is further impaired if indexed oligonucleotides are cross-contaminated or if indexed libraries are amplified in bulk. Double-indexing eliminates these problems and increases both the scope and accuracy of multiplex sequencing on the Illumina platform.

0 comments Cited 508 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Illumina sequencing library preparation for highly multiplexed target capture and sequencing.

Matthias Meyer, Martin Kircher (2010)

The large amount of DNA sequence data generated by high-throughput sequencing technologies often allows multiple samples to be sequenced in parallel on a single sequencing run. This is particularly true if subsets of the genome are studied rather than complete genomes. In recent years, target capture from sequencing libraries has largely replaced polymerase chain reaction (PCR) as the preferred method of target enrichment. Parallelizing target capture and sequencing for multiple samples requires the incorporation of sample-specific barcodes into sequencing libraries, which is necessary to trace back the sample source of each sequence. This protocol describes a fast and reliable method for the preparation of barcoded ("indexed") sequencing libraries for Illumina's Genome Analyzer platform. The protocol avoids expensive commercial library preparation kits and can be performed in a 96-well plate setup using multi-channel pipettes, requiring not more than two or three days of lab work. Libraries can be prepared from any type of double-stranded DNA, even if present in subnanogram quantity.

0 comments Cited 424 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Patterns of damage in genomic DNA sequences from a Neandertal.

Adrian W Briggs, Udo Stenzel, Philip L. F. Johnson … (2007)

High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms.

0 comments Cited 404 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Journal

Journal ID (nlm-ta): Philos Trans R Soc Lond B Biol Sci

Journal ID (iso-abbrev): Philos Trans R Soc Lond B Biol Sci

Journal ID (publisher-id): RSTB

Journal ID (hwp): royptb

Title: Philosophical Transactions of the Royal Society B: Biological Sciences

Publisher: The Royal Society

ISSN (Print): 0962-8436

ISSN (Electronic): 1471-2970

Publication date (Print): 23 November 2020

Publication date (Electronic): 05 October 2020

Publication date PMC-release: 05 October 2020

Volume: 375

Issue: 1812 , Theme issue ‘Insights into health and disease from ancient biomolecules’ compiled and edited by Anne C. Stone, Verena J. Schuenemann and Cecil M. Lewis

Electronic Location Identifier: 20190569

Affiliations

[1 ]Institute of Evolutionary Medicine, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland

[2 ]Vavilov Institute of General Genetics, Russian Academy of Sciences , Gubkina Street 3, Moscow 119991, Russia

[3 ]Laboratory of Plant Genomics, The Institute for Information Transmission Problems RAS , Moscow 127051, Russia

[4 ]Institute for Bioinformatics and Medical Informatics, University of Tübingen , Sand 14, 72076 Tübingen, Germany

[5 ]Museum and Institute of Zoology, Polish Academy of Sciences , Wilcza 64, Warsaw 00-679, Poland

[6 ]Centre of New Technologies, University of Warsaw , S. Banacha 2c, Warsaw 02-097, Poland

[7 ]Azov History, Archeology and Paleontology Museum-Reserve , Moskovskaya Street 38/40, Azov 346780, Russia

[8 ]Archaeological Museum in Gdańsk , Mariacka Street 25/26, Gdańsk 80-833, Poland

Author notes

e-mail: irina.morozova@ 123456iem.uzh.ch

e-mail: verena.schuenemann@ 123456iem.uzh.ch

One contribution of 14 to a theme issue ‘ Insights into health and disease from ancient biomolecules’.

Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.5096394.

Author information

Judith Neukamm http://orcid.org/0000-0001-8141-566X

Verena J. Schuenemann http://orcid.org/0000-0002-8593-3672

Article

Publisher ID: rstb20190569

DOI: 10.1098/rstb.2019.0569

PMC ID: 7702796

PubMed ID: 33012225

SO-VID: 2bc5f09b-dd66-4cee-8ffc-554b1cf19e3d

License:

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

History

Date accepted : 19 June 2020

Funding

Funded by: University of Zurich's University Research Priority Program “Evolution in Action: From Genomes to Ecosystems”;

Funded by: Mäxi Foundation, Switzerland;

Custom metadata

cover-date November 23, 2020

ScienceOpen disciplines: Philosophy of science

Keywords: plague,yersinia pestis,pathogen evolution,ancient pathogen genomics,ancient dna

Data availability:

ScienceOpen disciplines: Philosophy of science

Keywords: plague, yersinia pestis, pathogen evolution, ancient pathogen genomics, ancient dna

New ancient Eastern European Yersinia pestis genomes illuminate the dispersal of plague in Europe

Read this article at

Abstract

Related collections

Environment and Society Collection of The Rachel Carson Center and The White Horse Press

Most cited references 49

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

Illumina sequencing library preparation for highly multiplexed target capture and sequencing.

Patterns of damage in genomic DNA sequences from a Neandertal.

Author and article information

Journal

Affiliations

Author notes

Author information

Article

History

Funding

Categories

Custom metadata

Comments

Comment on this article

Similar content 755

Cited by 6

Most referenced authors 1,056