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Supplementary information to support : 'Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity'
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(2010) Supplementary information to support : 'Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity'. Nature Genetics, 42 (12). pp. 1140-1143. doi:10.1038/ng.705
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Plain Text
ExampleInputFilesForRScript1.txt - Supplemental Material Download (422b) |
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Other (R script)
RScript1.R - Supplemental Material Download (3811b) |
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Other (R script)
RScripts2.R - Supplemental Material Download (7Kb) |
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PDF
SupplementaryNote.pdf - Supplemental Material - Requires a PDF viewer. Download (49Kb) |
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Supplementary Fig. 1.1.pdf - Supplemental Material - Requires a PDF viewer. Download (729Kb) | Preview |
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Supplementary Fig. 2. Wordwide Map with All Strains Distribution.pdf - Supplemental Material - Requires a PDF viewer. Download (764Kb) | Preview |
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Supplementary Fig. 3. Pestis Routes Version 1.10.pdf - Requires a PDF viewer. Download (3853Kb) | Preview |
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Supplementary Fig. 4.1. Introduction into USA Version 1.10.pdf - Requires a PDF viewer. Download (1010Kb) | Preview |
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Supplementary Fig. 5. Madagascar Plague Expansion version 1.8.pdf - Requires a PDF viewer. Download (536Kb) | Preview |
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Supplementary Fig. 6. Madagascar Mutation Rate.pdf - Requires a PDF viewer. Download (225Kb) | Preview |
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Supplementary Fig. 7. Minimum Spanning Tree V1.1.pdf - Requires a PDF viewer. Download (347Kb) | Preview |
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Supplementary Fig. 8 Mean pairwise genetic distance.pdf - Requires a PDF viewer. Download (550Kb) | Preview |
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Supplementary Fig. 9 Distribution of allele frequencies during outbreaks.pdf - Requires a PDF viewer. Download (553Kb) | Preview |
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Supplementary Fig. 10 Accumulaion of SNPs with time.pdf - Requires a PDF viewer. Download (856Kb) | Preview |
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Microsoft Excel
Supplementary Table 1. List of genome sequences V1.2.xls Download (36Kb) |
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Microsoft Excel
Supplementary Table 2. Estimation of mutation rates from mutation discovery in Madagascar V1.2.xls Download (52Kb) |
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Microsoft Excel
Supplementary Table 3. Node assignments and strain sources V1.1.xls Download (77Kb) |
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Microsoft Excel
Supplementary Table 4. Properties of isolates from branch 1.ORI1 V1.1.xls Download (214Kb) |
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Microsoft Excel
Supplementary Table 5. SNPs in coding and intergenic regions from genomes alignment V1.1.xls Download (828Kb) |
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Microsoft Excel
Supplementary Table 6. SNPs in minimal spanning tree V1.1.xls Download (247Kb) |
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Microsoft Excel
Supplementary Table 7. Results of testing selected Pestoides isolates for certain SNPs V1.1.xls Download (48Kb) |
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Microsoft Excel
Supplementary Table 8. Minimal spanning tree branches and SNPs.V1.1.xls Download (63Kb) |
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Microsoft Excel
Supplementary Table 9. Excluded genomic regions according to CO92 positions Version1.4.xls Download (118Kb) |
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Microsoft Excel
Supplementary Table 10. Oligonucleotides used for 1.ORI1 strains genotyping V1.1.xls Download (52Kb) |
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Microsoft Excel
Supplementary Table 11. SNP calls based on sequencing Version1.2.xls Download (68Kb) |
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Microsoft Excel
Supplementary Table 12. SNPs that were excluded from the minimal spanning tree V1.1.xls Download (127Kb) |
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Supplementary Table 13. SNPs supporting earlier branching of strain Angola versus 91001 Version 1.3.xls Download (31Kb) |
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Supplementary Table 14. Genomes tree Dn Ds V1.1.xls Download (33Kb) |
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Supplementary Table 15. dHPLC gene fragments and oligonucleotides Version1.7.xls Download (109Kb) |
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Microsoft Excel
Supplementary Table 16. Sequenom assays Version 1.4.xls Download (375Kb) |
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Microsoft Excel
Supplementary Table 17. Discrepancies between Sequenom and dHPLC Version1.2.xls Download (52Kb) |
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Microsoft Excel
Supplementary Table 18. Oligonucleotides used for sequence validation Version1.4.xls Download (73Kb) |
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Archive (ZIP) (All supplementary tables and figures and the R script for the 2011 Nature Genetics manuscript)
Supplementary files.zip - Supplemental Material Download (8Mb) |
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 |
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| 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: |
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| 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. |
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| 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), | ||||
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