Total DNA from the Salmonella isolates was extracted using a TIANamp Bacteria DNA kits (Tiangen, Beijing, China) and then subjected to whole genome sequencing. The library was constructed using a Next® Ultra™ DNA Library Prep kit (New England Biolabs, Ipswich, UK) according to the manufacturer’s protocol, and 250-bp paired-end reads were obtained from an Illumina Hiseq2500 platform (Bionova Biotech Co., San Diego, CA, USA). For each isolate analyzed by Whole-Genome Sequencing, at least 100-fold coverage of raw reads were collected. A draft assembly of the sequences was generated using SOAPdenovo version 2.04 (http://soap.genomics.org.cn/soapdenovo.html ).
Assembled data, S. 4,[5],12:i:- strain SO4698-09 (RefSeq NZ_LN999997) were subjected to SNP calling and reference-based phylogeny tree building using CSI Phylogeny 1.4 [22 (link)] with SO4698-09 as the reference genome and default parameters for SNP filtering and pruning.
Assembled data, S. 4,[5],12:i:- strain SO4698-09 (RefSeq NZ_LN999997) were subjected to SNP calling and reference-based phylogeny tree building using CSI Phylogeny 1.4 [22 (link)] with SO4698-09 as the reference genome and default parameters for SNP filtering and pruning.
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