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Supplemental Material for Zaworski et al., 2021

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posted on 2021-06-30, 17:20 authored by Julie Zaworski, Oyut Dagva, Anthony W. Kingston, Alexey Fomenkov, Richard D. Morgan, Lionello Bossi, Elisabeth A. Raleigh

Table S1 "Pedigree LB5000 STK005" traces the descent of LB5000 and some relatives through the literature since 1959; with wild ancestor, donor strain, recipient strain, renaming, construction reference and mode of construction. File S1 "STK005 variants" contains 5 Excel spreadsheets documenting positions at which STK005 sequence differs from the genome sequences representing two ancestral components. For three genome segments derived from LT2, variant nucleotide positions of LT2 (NC_003197.2) are listed, with consequences for amino acid changes; for two short segments derived Salmonella enterica serovar Abony SW803 (H1, 15.4 kb and H2, 41.7 kb), all annotated loci are listed as well, since few positions vary from the Abony reference. The reference segments H1 and H2 were extracted from Salmonella enterica subsp. enterica serovar Abony str. 0014 - NZ_CP007534.1: for transduction 1 of Table S1, H1--nt 3956473-3942278 (reversed); for transduction 2, H2--nt 4713943-4725447(catenated)1-18493 (the segment crosses the numerical origin, so is catenated). File S2 "Analysis of 11 kb high-similarity region in the Gifsy prophages" describes and displays alignments (referred to as "Embedded figs") that resolve allele configurations in Gifsy prophages. File S3 "STK005 genotype inferences from sequence" describes the recorded genotype; explains assignment of flagellar genotype; accounts for IS element annotations in LT2 and STK005; describes the protocol used to generate the variant list found in File S1; lists protein changes that account for the genotype; and points out some additional possible changes. File S4 "PCR survey for 42bp insertion in isolates of S. enterica sv Typhimurium str LT2" demonstrates the insertion is present in Gifsy-1 and conserved in most LT2 strains.


Article title

Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium