The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse

Circle diagram of the DH10B genome. Protein-encoding genes are shown in the outer ring, with blue boxes representing those genes coded on the forward strand and gold boxes representing those on the complementary strand. Large deletions and insertions are indicated outside of the circle. In the next inner ring, IS elements that cause gene disruptions or are intergenic are indicated with red or aqua tick marks, respectively, with the positions above or below the line indicating which strand is transcribed. SNPs are then indicated with black tick marks. tRNAs (green tick marks) and small regulatory RNAs (purple tick marks) are shown, with those on the forward strand above the line and those on the complementary strand below it. Finally, rRNA operons are shown as red arrowheads.

Comparison of the DH10B and MG1655 genomes. Schematic of the two genomes showing colinear blocks of sequence. The endpoints of each block are defined by an adjacent sequence that is present only in one genome. The major structural rearrangements in DH10B are indicated below the genome representation.

Distribution of small-scale mutations in the DH10B genome. A schematic of the genome illustrated in Fig. 3 shows the distribution of SNPs and frameshifts (A) and positioning of IS elements (B). (A) Differences in the DH10B sequence affecting conserved domain sequences are indicated by asterisks, with different colors indicating the types of change. Green, silent SNP; red, missense SNP; black, nonsense SNP; yellow, frameshift. Genes in which the mutation has a known phenotypic consequence are indicated. Note that the frameshift in rph corrects the rph-1 allele present in MG1655. SNPs in intergenic regions are indicated with a caret, and at sites where more than a SNP is present, the number of changes is given. (B) IS-disrupted genes in common with MG1655 are indicated in black, while those unique to DH10B are in red. The specific IS element at each location is indicated; the disrupted gene is in parentheses. For clarity, only differences affecting gene regions are shown.

Comparison of φ80 and φ80dlacZΔM15 prophage structures. Diagrams of the two prophages show their chromosomal contexts and more-detailed schematics of the open reading frames (boxes) and major promoters within the two elements. Open reading frames above the center horizontal lines of the diagrams are transcribed in the forward direction, while those below the lines are coded on the complementary strand. Color boxes in the prophages indicate the source of the genes: yellow, φ80; blue, E. coli chromosome; green, Tn1000 from the F plasmid. The two types of terminal sequences, attP and res, are indicated, as is the lacZΔM15 allele. In φ80dlacZΔM15, the φ80 sequences end within gene 5 (indicated as 5′).