Theoretical distribution of DNA breaks and resulting sequencing templates near a telomere. The figure assumes that the shearing conditions were similar to those used in a typical genome sequencing project. Horizontal arrows represent sequencing reads derived from each end of a fragment whose termini correspond to the positions at which the original DNA strand broke under shearing stress. These positions are represented by vertical arrows. Breaks defining the two ends of a sequence template are connected with a curved line. The solid lines below the reads represent contigs resulting from assembly of the individual sequences. The breakpoint nearest to the telomere produces two DNA fragments, one telomeric and one subtelomeric. Both types of fragments potentially contain sequence information capable of linking the telomeric contig to the "internal" assembly. However, shearing the DNA to an average length of 4 kb should produce very few breaks in the region immediately adjacent to the telomere. Thus, the sequencing reads represented by dotted lines in (i) and (ii) are likely to be very rare. Furthermore, if a size-selection step is employed (as is typical for a genome project), the reads shown in (ii) will be further depleted. The scale at the top shows the distance from the telomere.
Schwartz and Farman BMC Genomics 2010 11:87 doi:10.1186/1471-2164-11-87