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. 2018 Oct 22;10(11):3089–3103. doi: 10.1093/gbe/evy236

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© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Fig. 2. — —Large structural variation events in experimentally evolved Bartonella genomes. (A) SmaI-PFGE run of Bartonella sp. OE 1-1 ancestral and evolved OE11-B3 genomes, showing a shift in the electrophoretic run of a high molecular band (red arrow), corresponding to a ∼30 kb molecular weight change in line OE11-B3. Lines corresponded to: 1. Salmonella enterica subsp. enterica serovar Braenderup (digested with XbaI, as a molecular marker); 2–3, Bartonella sp. OE 1-1 ancestral line (duplicates), and; 4–5, Bartonella sp. OE 1-1 line OE11-B3 (duplicates). (B) MAUVE alignments of whole-evolved and ancestral genomes evidencing a ∼33 kb region of the ancestral genome not covered in the evolved line (red-thick arrow). (C) SmaI-PFGE run of Bartonella sp. Tel Aviv ancestral and evolved genomes, showing a shift in the electrophoretic run of two high molecular-weight bands (∼320 and ∼130 kb) observed only in the evolved line TA-C2 (lines marked by pink arrows), and two bands (∼398 kb and ∼60 kb) which were not evident in this line, but present in the ancestors and other evolved lines. Lines corresponded to: 1&12: S. enterica subsp. enterica serovar Braenderup (digested with XbaI, as molecular marker); 2–3: Bartonella sp. Tel Aviv ancestral line; 4–5: Bartonella sp. Tel Aviv line TA-B2; 6–7: Bartonella sp. Tel Aviv line TA-C1; 8–9: Bartonella sp. Tel Aviv line TA-C2 (with a profile change: pink arrows); and, 10–11: Bartonella sp. Tel Aviv line TA-C3. (D) Whole genome comparison between ancestor and evolved lines, demonstrating a ∼800 kb inverted area in the evolved line. Figure was built using GenoplotR package in R software with the MAUVE alignment data. (E) Comparison of scaled coverage depth from Bartonella sp. Tel Aviv ancestor (triplicates) and evolved TA-B2 line in a 38,000 bp window. TA-B2 evolved line showed absence of reads covering a ∼13 kb region. (F) Conventional PCR amplification targeting the flanking sequences of the deletion detected in line TA-B2. A ∼7,000 bp product was obtained only in the TA-B2 line: L: GeneRuler High Range DNA Ladder; A: Bartonella sp. Tel Aviv ancestral strain; B1: Bartonella sp. Tel Aviv evolved TA-B1 line; B2: Bartonella sp. Tel Aviv evolved TA-B2 line; B3: Bartonella sp. Tel Aviv evolved TA-B3 line; EC: extraction control; NTC: nontemplate control. All gel pictures were color-inverted for clarity without any manipulation.