antibiotic resistance marker  (Addgene inc)

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex.

doi: 10.1073/pnas.2301394120

Figure Lengend Snippet: Fig. 1. Parallel evolution of SNVs and INDELs. (A) The distribution of homoplasy scores for 834,981 SNVs and 46,306 INDELs. 0.49% of SNVs have a homoplasy score ≥5 (P < 0.002) and 3.01% of INDELs have a homoplasy score ≥5 . (B) Proportion of INDELs with Hs ≥x for varying values of x, split into sets according to whether INDEL occurs within HT, SSR, or other region of the genome. (C and D) Homoplasy score (Hs) for 1,525 SNVs and 655 INDELs with homoplasy score ≥5 and minor (SNVs)/alternate (INDELs) allele frequency > 0.1% among 31,428 isolates, plotted against position on the genome. Bubble size corresponds to Hs. (C) INDELs broken down by whether they occur within an HT, SSR, or other region of the genome. HTs with a cumulative Hs score > 45 (across INDELs occurring within HT) are indicted by blue bars. (D) Variants colored in green occur within genes that have been associated with antibiotic resistance.

Article Snippet: A homopolymer frameshifting reporter was constructed from a hygromycin- resistant pDE43- MCtH vector, which is a version of pDE43MCK with a swapped antibiotic marker [Addgene plasmid #49523; (68)].

Techniques:

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex.

doi: 10.1073/pnas.2301394120

Figure Lengend Snippet: Fig. 2. Recency ratio for SNVs and HT INDELs. (A and B) The distribution of the ratio of (homoplasy score) to (# of isolates harboring the minor allele) for 1,208/1,525 SNVs (Fig. 1C) that occur in coding regions. (C) Breaking these SNV recency ratios down by gene category reveals higher ratios overall for antibiotic resistance genes when compared to other gene categories. (D and E) The distribution of the ratio of (homoplasy score) to (# of isolates harboring the alternate allele) for 100/655 INDELs (Fig. 1C) that occur in HT and coding regions. (F) Breaking these INDEL ratios down by gene category reveals higher ratios overall for antibiotic resistance genes when compared to other gene categories; however, the only two INDELs in this gene category were found in the HT of glpK. N = number of alleles, M = median RcR.

Article Snippet: A homopolymer frameshifting reporter was constructed from a hygromycin- resistant pDE43- MCtH vector, which is a version of pDE43MCK with a swapped antibiotic marker [Addgene plasmid #49523; (68)].

Techniques: