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. 2011 Oct 13;7(10):e1002282. doi: 10.1371/journal.ppat.1002282

Figure 7. Southern blot of CAPRE-estimated SSR lengths.

Figure 7

A) RFLP analysis of SalI fragments of PRV strains Kaplan (Ka), Becker (Be), Bartha (Ba), and a Becker stock passaged 10 times in vitro (Be p10). Positions of one standard marker are noted on the left; another marker lane is shown between the Bartha and Becker p10 lanes (5 bands: 23 kb, 9.4 kb, 6.6 kb, 2.3 kb, 2 kb). Asterisk (*) at 7 kb in the PRV Bartha lane highlights a size shift in the fragment containing the Bartha US-region deletion. B) Southern blot of the same fragments, using a biotinylated probe matching SSRKa17595 (a perfect 15-mer) to reveal the size of the SalI fragment containing this site. Without any SSR content, this fragment would be ∼0.55 kb in PRV Kaplan and Bartha, and ∼0.74 kb in PRV Becker. Based on observed fragment sizes, the 1 kb Kaplan and Bartha fragments each have ∼30 copies of this SSR, while the 2.5 kb average Becker fragment (range 1.6–3.5 kb) has on average ∼120 copies (range 58–184 copies). The variable fragment size in PRV Becker shifts upon passage in vitro (Be p10).