Fig. 1

Alignment of 01-B526 pAsa5 and pAsa9, and proposed recombination patterns for 01-B526 pAsa5. a The plasmid sequences were aligned and visualized using EasyFig [52]. Featured ORFs and regions were coloured using the following code: Red: transposases or transposase fragments, Blue: conjugative transfer proteins, Black: ORFs with detailed functions or domains, Cyan: hypothetical protein, Orange: TTSS structural genes; Light pink: TTS effectors and chaperones. This alignment shows that shared regions between pAsa5 and pAsa9 are also syntenic. Moreover, pAsa9 has its conjugative transfer genes in a single locus, compared to two loci with a traI repetition for pAsa5. Below the alignment, PCR targets locations used by Daher et al. to assess pAsa5 integrity at stressful growth temperature, and the resulting loss profile, are shown [17, 29]. b IS locations on 01-B526 pAsa5 allow for two types of recombination patterns: ISAS11-targetted, which was described previously [17], and ISAS5-targetted. ISAS11B-ISAS11C recombination leads to pAsa5 BC, which has lost its TTSS locus (top left circle). ISAS11A-ISAS11C recombination leads to pAsa5 AC, which has lost its TTSS and conjugative transfer loci (bottom left circle). However, in 01-B526-R4, the conjugative locus is detected by PCR since a similar copy is carried by pAsa9 (bottom left rectangles). ISAS5Z-ISAS5A recombination leads to pAsa5 ZA, which has also lost its TTSS and conjugative transfer loci (right circle). Again, in this case the pAsa9 conjugative locus is detected by PCR, effectively masking the deletion