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Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica. Archive package of additional figures, tables and data
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Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica. Archive package of additional figures, tables and data. [Dataset]
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Archive (ZIP) (Package of additional figures, tables and data)
Additional Figures, Tables and Data.zip - Published Version Available under License Creative Commons Attribution 4.0. Download (65Mb) |
Official URL: http://wrap.warwick.ac.uk/101808
Abstract
Salmonella enterica serovar Paratyphi C is the causative agent of enteric (paratyphoid) fever. While today a potentially lethal infection of humans that occurs in Africa and Asia, early 20th century observations in Eastern Europe suggest it may once have had a wider-ranging impact on human societies. We recovered a draft Paratyphi C genome from the 800-year-old skeleton of a young woman in Trondheim, Norway, who likely died of enteric fever. Analysis of this genome against a new, significantly expanded database of related modern genomes demonstrated that Paratyphi C is descended from the ancestors of swine pathogens, serovars Choleraesuis and Typhisuis, together forming the Para C Lineage. Our results indicate that Paratyphi C has been a pathogen of humans for at least 1,000 years, and may have evolved after zoonotic transfer from swine during the Neolithic period.
| Item Type: | Dataset | |||||||||||||||
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| Subjects: | Q Science > QR Microbiology | |||||||||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School | |||||||||||||||
| Type of Data: | ZIP | |||||||||||||||
| Library of Congress Subject Headings (LCSH): | Typhoid fever -- Genetic aspects -- History, Typhoid fever -- Trondheim (Norway) -- 13th century | |||||||||||||||
| Publisher: | University of Warwick, Warwick Medical School | |||||||||||||||
| Official Date: | 4 May 2018 | |||||||||||||||
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| Status: | Not Peer Reviewed | |||||||||||||||
| Publication Status: | Published | |||||||||||||||
| Media of Output (format): | .pdf .xlsx .txt .nex | |||||||||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||||||||
| Copyright Holders: | University of Warwick | |||||||||||||||
| Description: | Package of additional information contains: Ancestral reconstruction 1 - Maximum likelihood phylogeny and geographical origins derived from 61,451 non-repetitive core SNPs within the Para C Lineage plus Birkenhead Ancestral reconstruction 2 - Geographic inference of the sources of clades within the Para C Lineage Concoct 1 - Single core gene (SCG) frequencies in the 76 CONCOCT clusters generated after binning contigs Concoct 2 - Statistics after clustering all metagenomes with MEGAHIT Concoct 3 - Taxonomic assignments for 11 metagenome assembled genomes (MAGs) Concoct 4 - Single-stranded deamination rates for Ragna, human DNA and 11 MAGs Concoct 5 - Genomic coverage of 11 MAGs by source and sequencing library Concoct 6 - Bacterial taxa found by Kraken in SK152 metagenomes at ≥ 0.02% frequency. Concoct 7 - Eleven MAGs Contigs. Concoct 8 - Alignments and phylogenies of SCGs across the Tree of Life. Date estimation 1 - Date randomization tests for the temporal signal in multiple replicate data sets that were analysed by BEAST Date estimation 2 - Linear regression plots (TempEst [37]) of root-to-tip genetic distances to the MRCA of two sets of modern genomes plus Ragna (red), Tepos-14 and Tepos-35 (green) [19] versus their dates of sampling. Date estimation 3 - Comparison of MRCA dating estimates by BEAST using ancient plus modern, and only modern strains Date estimation 4 - Raw Maximum Clade Credibility trees as well as a summary of the mutation rates from BEAST inferences. ParaC Pan-genome 1 - Gain and loss of genomic islands shown on a maximum-likelihood radial phylogeny derived from 61,451 non-repetitive core SNPs within the Para C Lineage plus Birkenhead ParaC Pan-genome 2 - Summary statistics for pan-genomic contents of Ragna plus 219 modern genomes of the Para C Lineage ParaC Pan-genome 3 - Gene gain/loss events and numbers of pseudogenes by sub-lineage ParaC Pan-genome 4 - The pan-genome of the Para C Lineage based on 6,665 single copy genes from 220 genomes. ParaC Pan-genome 5 - Sequences, original gene names and annotations of the reference sequences for 6,665 pan genes in the ParaC Pan-genome 6 - Pseudogenes associated with sub-lineages and clades of the Para C Lineage. ParaC Pan-genome 7 - Genomic islands and plasmids. ParaC Pan-genome 8 - Data and script for extracting rate of gene gain/loss and pseudogenes from the branches of an ML tree. See readme.txt for instructions. ParaC genome SNPs 1 - Numbers of mutational and recombinational SNPs per clade within the Para C Lineage plus Birkenhead ParaC genome SNPs 2 - SNPs in the core genome of the Para C Lineage plus Birkenhead. ParaC genome SNPs 3 - Maximum likelihood phylogeny and inferred geographical origins based on 61,451 non-repetitive core SNPs from the Para C Lineage plus Birkenhead. ParaC genome SNPs 4 - Venn diagram of substitutions scored as recombinational by RecHMM, ClonalFrameML and Gubbins. Salmonella supertree 1 - Metadata for 2,964 representative genomes in Salmonella enterica subsp. I. Salmonella supertree 2 - A species tree (ASTRID) based on 3,002 core gene trees from 2,964 representative genomes from S. enterica subsp. I. Salmonella supertree 3 - A RAxML maximum likelihood phylogeny based on a 2.8 Mbp concatenate of 3,002 core genes from 2,964 representative genomes from S. enterica subsp. I Workflow - Workflow to reconstruct the Ragna genome |
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| Date of first compliant deposit: | 2 May 2018 | |||||||||||||||
| Date of first compliant Open Access: | 2 May 2018 | |||||||||||||||
| RIOXX Funder/Project Grant: |
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