DIFFERENCE BETWEEN HIERARCHICAL SHOTGUN APPROACH AND

WHOLE GENOME SHOTGUN APPROACH

Hierarchical shotgun sequencing is a two-step process of sequencing the

genome, this includes: physical mapping and sequencing. This approach
starts with a well-defined physical mapping. The markers of the genome
regions are identified. The genome will then be broken/sheared into larger
fragments using restriction enzymes. These fragments are cloned in bacteria
using bacterial artificial chromosomes (BAC), and the inserts are isolated, thus,
the whole genome is mapped by finding markers. Furthermore, the fragments
are again sheared randomly into smaller fragments. These fragments are
individually sequenced, and are aligned so that identical sequences are
overlapping. Thus, the genome is assembled based on the physical map.
Meanwhile, the whole-genome shotgun sequencing is a one-step process,
bypassing the mapping stage, and going directly to the sequencing stage. The
entire genome is sheared randomly into variable-sized fragments using
restriction digestion, followed by cloning. The sequencing starts with a set of
BAC clones, which contains very large DNA inserts. Each insert is sequenced
on both ends, and the sequences will serve as an identity tag. The sequences
are ordered by their overlaps, producing the sequence of the whole genome.