Mycobacterial transconjugant genomes are complex mosaics of their parental strains.

<p>(A) Conjugation and genome comparison protocol. Sequence reads for each transconjugant were aligned with the reference donor genome and viewed with IGV. Columns of colored nucleotides mark informative SNPs between the recipient and donor strains, while random colored nucleotides indicate sequence errors. (B) A Circos plot depicts the mosaic nature of 12 <i>M. smegmatis</i> transconjugant genomes. mc²155 donor DNA segments (alternating blue and magenta, or green) replaced homologous recipient sequences (yellow). Positions of integrated kanamycin genes (<i>Km</i>) are shown around the periphery (green arrows), and transferred donor DNA segments containing the <i>Km</i> gene are shown in green. Strain nomenclature is based on the genomic location of the <i>Km</i> gene in Mb, thus Km0.1 is inserted at coordinate 0.1 Mb in mc²155. Strains are from outer to inner circle, respectively: Km6.9e, Km0.1f, Km6.9d, Km3.2, Km6.9c, Km0.1e, Km3.8, Km4.5b, Km2.2a, Km0.1d, Km0.1c, and Km6.4a. The innermost circle is a compilation of all segments of mc²155 DNA, showing that almost all regions of the donor chromosome were transferred despite the small sample size. (C) Microcomplexity of parental SNP profiles at some transconjugant recombination sites. Compiled sequence read landscapes are shown for mc²874 and one transconjugant (Km6.9e) aligned to the mc²155 sequence (top) for a 1 kb segment of the genome (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio.1001602.s008" target="_blank">Table S2</a>, coordinates 470,385–471,385). The presence of informative SNPs (each color represents a different base) indicates recipient sequences, while segments lacking SNPs define donor sequence. Accordingly, parental genotype segments are shown in the schematic below with recipient (yellow) and donor (blue and magenta) genotypes interspersed throughout this 1 kb region. Note that rare cases of isolated recipient SNPs in our designated donor segments are excluded by our stringent criterion requiring two consecutive SNPs to conclusively establish parental origin. The lower panel shows the same sequences aligned to the mc²874 sequence, in which the SNPs now indicate donor sequence. This reciprocal alignment confirms the assignment of donor and recipient sequences in the schematic map.