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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 Zhemin Zhou (157214) Inge Lundstrøm (24893668) Alicia Tran Dien (24899239) Sebastián Duchêne (110910) Nabil-Fareed Alikhan (5066198) Martin J. Sergeant (24732832) Gemma Langridge (3549053) Anna K. Fotakis (4066471) Satheesh Nair (157213) Hans K. Stenøien (8811296) Stian S. Hamre (24893671) Sherwood Casjens (55674) Christopher Quince (178494) Axel Christophersen (9257291) Nicholas R. Thomson (6811496) François-Xavier Weill (157212) Simon Ho (787728) M. Thomas P. Gilbert (7247759) Mark Achtman (126786) Typhoid fever -- Genetic aspects -- History Typhoid fever -- Trondheim (Norway) -- 13th century Migrated from ePrints 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.<br><br>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 Para C Lineage. 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 2018-05-04T00:00:00Z Dataset Dataset 10.82444/warw.33756232.v1 https://figshare.com/articles/dataset/Data_for_Millennia_of_genomic_stability_within_the_invasive_Para_C_Lineage_of_Salmonella_enterica_Archive_package_of_additional_figures_tables_and_data/33756232 CC BY 4.0