What is the Difference Between Hierarchical and Whole Genome Shotgun Sequencing?

Hierarchical and whole-genome shotgun sequencing are two approaches used to sequence large genomes. The main differences between these techniques are:

1. Fragment size: In hierarchical shotgun sequencing, the genome is first broken into larger fragments, while in whole-genome shotgun sequencing, the entire genome is broken into small fragments for sequencing.
2. Two-step vs. one-step process: Hierarchical shotgun sequencing is a two-step process, where the genome is broken into larger fragments, and then the order of these segments is deduced. In contrast, whole-genome shotgun sequencing is a single-step process, where the entire genome is broken into small fragments and sequenced.
3. Low-resolution map: Hierarchical shotgun sequencing involves creating a low-resolution map of the genome before actual sequencing. This step is not present in whole-genome shotgun sequencing.
4. Sequencing method: In hierarchical shotgun sequencing, genomic DNA is cut into pieces of about 150 Mb and inserted into BAC vectors, which are then transformed into E. coli for replication and storage. The BAC inserts are isolated and mapped to determine the order of each cloned 150 Mb fragment. In whole-genome shotgun sequencing, genomic DNA is randomly sheared into small pieces, cloned into plasmids, and then sequenced.
5. Speed and labor intensity: Hierarchical shotgun sequencing is slower and more labor-intensive than whole-genome shotgun sequencing due to the extensive BAC library creation and tiling path selection.

In summary, hierarchical shotgun sequencing involves breaking the genome into larger fragments and creating a low-resolution map before sequencing, while whole-genome shotgun sequencing directly breaks the entire genome into small fragments for sequencing. Hierarchical sequencing is slower and more labor-intensive, but it relies less heavily on computer algorithms than whole-genome shotgun sequencing.

Comparative Table: Hierarchical vs Whole Genome Shotgun Sequencing

Here is a table comparing the differences between hierarchical and whole genome shotgun sequencing:

In summary, hierarchical shotgun sequencing involves sequencing large fragments in a step-by-step manner, while whole genome shotgun sequencing involves sequencing small fragments without a mapping step. The former requires creating a low-resolution physical map before sequencing, whereas the latter bypasses the mapping step. The assembly process in hierarchical sequencing is less efficient compared to whole genome shotgun sequencing.