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Shotgun Sequencing (SGS)

Structural Determination Techniques (DNA, RNA and Protein)

  1. Jun Yu,
  2. Gane Ka-Shu Wong,
  3. Jian Wang,
  4. Huanming Yang

Published Online: 15 SEP 2006

DOI: 10.1002/3527600906.mcb.200400136

Reviews in Cell Biology and Molecular Medicine

Reviews in Cell Biology and Molecular Medicine

How to Cite

Yu, J., Wong, G. K.-S., Wang, J. and Yang, H. 2006. Shotgun Sequencing (SGS). Reviews in Cell Biology and Molecular Medicine. .

Author Information

  1. Beijing Genomics Institute, Beijing & James D. Watson Institute of Genome Sciences, Hangzhou, China

Publication History

  1. Published Online: 15 SEP 2006


Shotgun sequencing (SGS) is primarily a large-scale sequencing (LSS) technique that does not rely on precise guiding information about the target DNA, which includes large-insert clones and single genomes, ranging from thousands of basepairs (Kb) to billions of basepairs. A mixture of smaller genomes can also be sequenced in a similar way when retrospective means are available to assemble and distinguish them. It provides a fast and cost-effective way of sequencing large genomes regardless of whether the project as a whole takes a “whole-genome” (WG) or “clone-by-clone” (CBC) approach. The success of SGS essentially depends on random sampling, high-quality data, sufficient sequence coverage, effective assembly, and gap closing procedures. SGS has already demonstrated its tremendous power in sequencing not only microbial genomes but also large eukaryotic genomes, such as those of the cultivated rice and the laboratory mouse. Together with improved sequencing technologies and computing tools, SGS is expected to play a central role in the field of genomics, especially when the latter has to constantly face some major challenges, scientific, managerial, and political. Some of the scientific challenges relate to the effective sequencing of large, polyploid, and mixed genomes, as well as those with highly repetitive sequence contents. A key managerial challenge is for the operators to consistently produce high-quality data while increasing throughput and reducing cost. It is always a tough decision for a steering committee organizing a genome project to choose between WG and CBC, but SGS is always the basic technique of choice.


  • Large-insert Clones;
  • Minimal-tiling-path Clones;
  • Physical Gap;
  • Physical Map;
  • Scaffold;
  • Sequence Contig;
  • Sequence Gap;
  • Shotgun Sequencing