Further details on SNPs and indels in HN878 (Table S2) relative to H37Rv, including IS6110 transpositions (Table S3) are described in the Additional file 1.
We also compare HDA⁎ to Transposition-table Driven Scheduling (TDS), a hash-based parallelization of IDA⁎, and show that, in planning, HDA⁎ significantly outperforms TDS.
We then amplified DNA flanking both ends of the integrated plasmid sequence by inverse PCR [31], for each of the 28 transposition products (Table S1).
Interestingly, IS H6 preferentially targets an AT-rich motif (AANATNTT) that is duplicated upon transposition (supplementary table S2 and fig. S1, Supplementary Material online).
The same considerations regarding the use of isogenic lines containing the same Ds reporter apply to the present study wherein significant differences in Ac transposition frequencies are documented (Table 1, Table S3, Table S4).
These selected and screened clones were tentatively defined as transposition clone candidates (Table S1).
We identified 10,964 deletions, 1,239 insertions and 547 other SVs such as duplication, inversion and transposition by resequencing (Table 1).
Both the outbreak isolates had upregulated genes involved in transport and efflux, restriction modification, and transposition as follows (Table 5).
Our update to TAIR10 retained 4,539 loci clearly referenced to transposition events (supplementary table S1, Supplementary Material online), illustrating a 14% average for GTD genes among protein-coding loci in Arabidopsis (fig. 2 B).
Up-regulated genes fell into three main functional categories: Genes related to ribosome assembly and metabolism, Ty transposition, and proteolytic processes (Table 2).
