Supplementary information to support : 'Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity'

Morelli, Giovanna, Song, Yajun, Mazzoni, Camila J., Eppinger, Mark, Roumagnac, Philippe, Wagner, David M., Feldkamp, Mirjam, Kusecek, Barica, Vogler, Amy J., Li, Yanjun et al.
(2010) Supplementary information to support : 'Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity'. Nature Genetics, 42 (12). pp. 1140-1143. ISSN 1061-4036 doi:10.1038/ng.705

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[thumbnail of Supplementary Table 1. List of genome sequences V1.2.xls] Microsoft Excel
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[thumbnail of Supplementary Table 5. SNPs in coding and intergenic regions from genomes alignment V1.1.xls] Microsoft Excel
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[thumbnail of Supplementary Table 7. Results of testing selected Pestoides isolates for certain SNPs V1.1.xls] Microsoft Excel
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[thumbnail of Supplementary Table 8. Minimal spanning tree branches and SNPs.V1.1.xls] Microsoft Excel
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[thumbnail of Supplementary Table 9. Excluded genomic regions according to CO92 positions Version1.4.xls] Microsoft Excel
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Abstract

Plague is a pandemic human invasive disease caused by the bacterial agent Yersinia pestis. We here report a comparison of 17 whole genomes of Y. pestis isolates from global sources. We also screened a global collection of 286 Y. pestis isolates for 933 SNPs using Sequenom MassArray SNP typing. We conducted phylogenetic analyses on this sequence variation dataset, assigned isolates to populations based on maximum parsimony and, from these results, made inferences regarding historical transmission routes. Our phylogenetic analysis suggests that Y. pestis evolved in or near China and spread through multiple radiations to Europe, South America, Africa and Southeast Asia, leading to country-specific lineages that can be traced by lineage-specific SNPs. All 626 current isolates from the United States reflect one radiation, and 82 isolates from Madagascar represent a second radiation. Subsequent local microevolution of Y. pestis is marked by sequential, geographically specific SNPs.

Item Type: Journal Item
Alternative Title: Phylogenetic diversity and historical patterns of pandemic spread of Yersinia pestis
Subjects: Q Science > QR Microbiology
Divisions: Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection
Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School
Library of Congress Subject Headings (LCSH): Plague -- Genetic aspects, Yersinia pestis , Phylogeography
Journal or Publication Title: Nature Genetics
Publisher: Nature Publishing Group
ISSN: 1061-4036
Official Date: 2010
Dates:
Date
Event
2010
Published
Volume: 42
Number: 12
Page Range: pp. 1140-1143
DOI: 10.1038/ng.705
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access
Description:

All the supplementary tables and figures and the R script for the 2011 Nature Genetics manuscript.
Date of first compliant deposit: 5 October 2016
Date of first compliant Open Access: 5 October 2016
Funder: Germany. Deutsch Sanitätstruppe [German Medical Corps], Science Foundation Ireland (SFI), National Key Program for Infectious Diseases of China, State Key Development Program for Basic Research of China, United States. Department of Homeland Security, National Institutes of Health (U.S.) (NIH), Wellcome Trust (London, England), Centers for Disease Control and Prevention (U.S.) (CDC)
Grant number: MSAB15A013 (Deutsch Sanitätstruppe), 05/FE1/B882 (SFI), 2008ZX10004009 (Key Program for Infectious Diseases), 2009CB522600 (Basic Research), NBCH2070001; HSHQDC-08- C00158 (Homeland Security), AI065359, N01AI-30071 (NIH),
Related URLs:
URI: https://wrap.warwick.ac.uk/81946/

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