Fig. 9

Strand-biased attL × attR recombination of putative SEs. a SE-VanAT68554 from V. anguillarum. (i) Comparison of the genome structures based on blastn. Primers used for att sites detection PCR were depicted by numbered triangles. (ii) Results of the att site detection PCR. The primer set used was 1–2 for attL, 3–4 for attR, 2–3 for attS, and 1–4 for attB. (iii) Alignment of attL, attB, and attR. Only the top strand is shown. SE region is shown in orange. The expected attS sequences (T strand exch, top strand exchange product; B strand exch, bottom strand exchange products) are shown below the alignment with their observed number of Illumina reads. The black triangle indicates the putative nicking site in attL × attR recombination. b SE-ValAT17749 from V. alginolyticus. c SE-Pda04Ya311 from the Photobacterium plasmid pAQU1. Genomic DNA extracted from E. coli W3110rif carrying pAQU1 was used as the template. d SE-PpuAT51753 from S. putrefaciens. Note that IS was inserted into the attR region. Takara Wide range DNA ladder (Takara Bio, Shiga, Japan) was used as ladder marker across panels