Genome Sequencing

Abstract

Genome sequencing determines the order of the DNA bases in an organism. The method of choice for genome sequencing is based on chain termination sequencing and the random shotgun strategy.

Keywords: DNA sequencing; shotgun; dideoxy chain termination sequencing; human genome sequence; whole genome assembly

Figure 1.

Sanger chain termination sequencing method. Comparison of the chemical structures of 2′‐deoxynucloside triphosphate and 2′, 3′‐dideoxynucloside triphosphate. Note the substitution of the 3′ hydroxyl group by a hydrogen in the dideoxy form, which prevents extension of the nascent DNA chain 5′ to 3′.

Figure 2.

Schematic of the chain termination method as implemented with fluorescent detection of the four dideoxynucleotides. See text for further explanation. Because the sequence is read from newly synthesized fragments, it corresponds to the complementary strand of the initial template.

Figure 3.

Hierarchical shotgun versus whole‐genome shotgun, or top‐down versus bottom‐up, showing the different features of hierarchical mapping and shotgun sequencing and whole‐genome shotgun strategies. In the hierarchical, top‐down approach, the genome is progressively broken down into smaller segments. Initially, long‐range framework maps were derived by genetic mapping of microsatellites and radiation hybrid mapping of any marker that could be amplified by polymerase chain reaction. Then the genome was organized in overlapping contigs of clones, notably BACs, which were positioned relative to the framework maps. The genome sequence is achieved by shotgun sequencing of single BACs sufficient to cover the entire map. In the whole‐genome shotgun approach (bottom‐up), the genome is randomly cloned directly into the sequencing vector. Sufficient clones are sequenced to provide five‐ to tenfold coverage of the entire genome and the genome sequence is assembled in a single step. The use of sequences from both ends of inserts of defined size provides paired reads that assist the assembly and link across gaps.

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Further Reading

Bishop JE and Waldholz M (1990) Genome. New York, NY: Simon and Schuster.

Cook‐Deegan R (1994) The Gene Wars: Science, Politics, and the Human Genome. New York, NY: WW Norton & Company.

Davies K (2001) Cracking the Genome: Inside the Race to Unlock Human DNA. New York, NY: Simon & Schuster.

Green ED, Birren B, Klapholz S, Myers RM and Hieter P (eds.) (1999) Genome Analysis: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.

Kevles DJ and Hood L (eds.) (1992) The Code of Codes: Scientific and Social Issues in the Human Genome Project. Cambridge, MA: Harvard University Press.

Sinsheimer RL (1989) The Santa Cruz Workshop – May 1985. Genomics 5: 954–956.

Sulston J and Ferry G (2002) The Common Thread – A Story of Science, Politics, Ethics and the Human Genome. London, UK: Bantam Press.

Venter JC, Adams MD, Myers EW, et al. (2001) The sequence of the human genome. Science 291: 1304–1351.

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How to Cite close
Dunham, Ian(Sep 2005) Genome Sequencing. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005378]