Are there known genome sequencing issues in E. coli?
Generally, gaps in genomes occur due to failure of de novo assembly -- the DNA can be sequenced accurately, but cannot subsequently be placed into a contiguous assembly due to alignment ambiguity with adjacent sequences.  In eukaryotes, telomeres and centromeres are difficult to assemble from short reads because they are highly repetitive. In bacteria, repetitive regions of the genome can cause similar problems when assembling from short reads.  Such regions include CRISPR arrays, integrated mobile elements (e.g. transposons), and gene duplications.1,2
So, what made a short-read no-gap assembly of E. coli strain C difficult, specifically? Alignment of the original short-read assembly 3 to the long-read reference 4 with Mauve 5 gives positions and length of gaps.

The first gap in the ordered short-read assembly (left-most red line in the figure) occurs at position 15,085 in the first contig and is 320 bp long. Looking at the same region in the long-read assembly, this closely corresponds to a 236 bp tandem repeat (CTGG × 59) at position 14,848. The authors of the short-read paper used 150 bp paired-end MiSeq reads to create their assembly, which, after adapter trimming, would likely not give enough sequence context flanking the repeat region to span it with a single read, thus creating a gap. This is just one example, and the rest of the gaps could also be repeats or other aforementioned mobile elements.


Treangen TJ, Abraham AL, Touchon M, Rocha EP. Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev. 2009 May;33(3):539-71.
Ricker N, Qian H, Fulthorpe RR. The limitations of draft assemblies for understanding prokaryotic adaptation and evolution. Genomics. 2012 Sep;100(3):167-75.
https://www.ncbi.nlm.nih.gov/nuccore/MNKV00000000
https://www.ncbi.nlm.nih.gov/nuccore/CP029371
Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004 Jul;14(7):1394-403.