The key difference between hierarchical and whole genome shotgun sequencing is that in hierarchical shotgun sequencing, the genome is broken into larger fragments prior to sequencing while, in whole genome shotgun sequencing, the entire genome is broken into small fragments for sequencing.
Sequencing is an important technique in molecular processes, especially in the accurate identification of species. In fact, it is the technique of identifying the precise order of nucleotides in a gene or a genome. There are many techniques for sequencing. Some of these include Maxam Gilbert Method, Sanger Method and automated Sanger method.
CONTENTS
1. Overview and Key Difference
2. What is Hierarchical Shotgun Sequencing
3. What is Whole Genome Shotgun Sequencing
4. Similarities Between Hierarchical and Whole Genome Shotgun Sequencing
5. Side by Side Comparison – Hierarchical vs Whole Genome Shotgun Sequencing in Tabular Form
6. Summary
What is Hierarchical Shotgun Sequencing?
Hierarchical Shotgun sequencing is one method of sequencing. It is also called ‘top-down sequencing’. Further, this method consists of two steps: the first step is genome amplification, and the second step is genome fragmentation. In this method, the genome is sheared into large fragments first. It is followed by the cloning of these large fragments into various hosts using vectors or artificial chromosomes. Then, these recombinant vectors are arranged into a library. During the shotgun sequencing, the recombinant vector clones undergo sequencing individually. The fragments in the clones undergo restriction digestion to further reduce the size of the genome, thereby undergoing sequencing.
Figure 01: Hierarchical Shotgun Sequencing
During hierarchical shotgun sequencing, the large chunks of fragments have to be arranged in order, prior to the shotgun sequencing. It takes place with the aid of the molecular markers that are incorporated during the cloning process.
Hierarchical shotgun sequencing creates a low-resolution gene map. But it creates an ordered sequence map. Thus, it takes a longer duration than direct sequencing. The whole process delays due to the creating of a recombinant vector library. Is it also a labour-intensive technique. However, at present, the technique is automated to ease the work.
What is Whole Genome Shotgun Sequencing?
Whole genome shotgun sequencing is a single step sequencing process. In this process, the whole genome shearing takes place first. Following this, each of these small fragments undergoes sequencing randomly. Upon completion of the sequencing, the sequences analysis takes place. During sequence analysis, the overlapping sequences are removed, and the analysis is not an ordered process. Therefore, the assembly of sequences is a less efficient process in comparison to hierarchical shotgun sequencing. However, the process of whole genome shotgun sequencing is more rapid, and the analysis of the whole genome can take place at a single instance.
What are the Similarities Between Hierarchical and Whole Genome Shotgun Sequencing?
- Hierarchical and whole genome shotgun sequencing are two sequencing approaches.
- Both undergo Sanger sequencing or automated Sanger sequencing methods.
- They are involved in sequencing DNA and RNA fragments.
- Moreover, both methods are important in molecular diagnostics and research purposes.
- At present, both techniques are automated or computer-based.
- Both techniques rely on the fragmentation of the genome.
What is the Difference Between Hierarchical and Whole Genome Shotgun Sequencing?
Hierarchical shotgun sequencing generates larger sized fragments in comparison to whole-genome shotgun sequencing, which works with small fragments of sequences. So, this is the key difference between hierarchical and whole genome shotgun sequencing. Besides, the hierarchical shotgun sequencing consists of two major steps, while the whole-genome shotgun sequencing relies on one major step.
Furthermore, another difference between hierarchical and whole genome shotgun sequencing is that the resolution is higher in whole-genome shotgun sequencing in comparison to hierarchical shotgun sequencing.
The below infographic summarizes the difference between hierarchical and whole genome shotgun sequencing.
Summary – Hierarchical vs Whole Genome Shotgun Sequencing
Hierarchical and whole-genome shotgun sequencing are two techniques to sequence large genomes. The hierarchical shotgun sequence is a two-step process of sequencing where the genome is broken into larger fragments. In contrast, the whole-genome shotgun sequencing is a single step sequencing where the genome is broken into small fragments and directly sequenced. Thus, this is the key difference between hierarchical and whole genome shotgun sequencing. Moreover, the technical aspects may vary among the two techniques.
Reference:
1. Waterston, Robert H, et al. “On the Sequencing of the Human Genome.” Proceedings of the National Academy of Sciences of the United States of America, The National Academy of Sciences, 19 Mar. 2002, Available here.
2. Pal, Shital. “Genome Sequencing.” LinkedIn SlideShare, 4 Nov. 2014, Available here.
Image Courtesy:
1. “Whole genome shotgun sequencing versus Hierarchical shotgun sequencing” By Commins, J., Toft, C., Fares, M. A. – “Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects.” Biol. Procedures Online (2009). Accessed via SpringerImages (CC BY-SA 2.5) via Commons Wikimedia