Blakesley et al. BMC Genomics 2010, 11:21 http://www.biomedcentral.com/1471-2164/11/21 Page 10 of 15 bacterial host: E. coli DH10B tonA). Aliquots of the liga- tion reactions, which earlier produced the initial shotgun libraries, were used to separately transform competent cells of copy-control E. coli strain EPI400 (Epicentre Biotechnologies); BAC sequencing was then performed per our usual routine, after which we compared assem- blies from sequence reads obtained with each host strain. Representative results from those comparisons are shown in Figure 4 for a portion (~ 20 to 60 kb) of each of the three BACs. Note the greater uniformity in sequence-read redundancy obtained with the copy-con- trol host strain and the elimination of gaps in two of the BAC sequences. Based on these initial findings, we performed a similar study with eight additional BACs. Using our standard host strain, the sequence assembly of each of these clones had ≥ 5 uncaptured gaps (Table 5). An additional two BACs [GenBank:AC190000 and GenBank: AC188356] (see Table 5) were included as controls, with their sequence assemblies having 2 and 0 uncaptured Figure 4 Variation in the redundancy of sequence reads generated using shotgun libraries prepared with standard and copy-control E. coli strains. A shotgun-subclone library was prepared from each of three BACs [GenBank:AC153092, AC190087, and AC186717] and used to transform either standard DH10B tonA (Std) or copy-control EPI400 (CC) E. coli strains. From each library, paired forward and reverse sequence reads were then generated from randomly selected subclones to produce assemblies that provided an average of eightfold sequence redundancy. Aligned representative regions of the assemblies that highlight differences in sequence redundancy encountered with the two E. coli strains are shown for each BAC. Yellow lines indicate sequence-read redundancies on the upper and lower strands of the indicated sequence contig (black/red line); the horizontal orange lines depict a redundancy value of 10.