Shotgun sequencing breaks DNA into small fragments, clones, sequences and assembles them using computer analysis. Developed by Craig Venter, it competed with the Human Genome Project’s map-based sequencing. Whole genome sequencing bypasses mapping and starts with DNA sequencing, resulting in a contig. Shotgun sequencing is now the preferred method for genome sequencing.
Shotgun sequencing is a DNA sequencing method whereby a long stretch of DNA is physically broken into small fragments (approximately 2,000 base pairs) which are cloned, sequenced and assembled using computer analysis. It was developed and popularized by Craig Venter of Celera Corporation. Venter developed the technique in 1996 while working at the Institute for Genome Research.
Venter founded Celera in 1998 with a mission to sequence the human genome within three years. This goal competed directly with the already operational Human Genome Project, a consortium of universities working together to sequence the human genome using an older strategy called map-based sequencing, or BAC-to-BAC. This method involved first breaking the genome into 150,000 base pair pieces called BACs, assembling the BACs in order, and then detailed sequencing each BAC.
Whole genome sequencing bypasses the creation and mapping of BACs and starts right with DNA sequencing. The process begins with taking a sample of high molecular weight DNA from the organism of interest and physically breaking it into small pieces by passing it through a narrow-gauge syringe or by sonicating it, one way of breaking up the sample using sound waves. Cutting is a random process, so the sequences of the fragments will have some overlap with each other. Cutting does not specifically create the 2,000 base pair fragments needed for sequencing, but fragments of the desired size must be purified from the mix.
The next step is to join the DNA fragments with carrier DNA called vector. This process is known as cloning and creates a sequencing library from which an entire genome will be sequenced. The sequence of each clone in the library is determined and computer analysis is used to find overlapping or continuous sequences in each fragment. The assembly of the overlaps creates a contig, which is a long continuous stretch of DNA sequence.
Cloning the shotgun will usually result in some gaps between contigs because some sequences are accidentally missing from the library. The gaps can be filled by creating a new library or by using known sequences to extend outward from the contig. Because shotgun sequencing sequencing DNA fragments randomly, many fragments are sequenced more than once, creating greater certainty that the sequence is correct than if each fragment had been sequenced only once or twice.
The human genome was sequenced both by the Human Genome Project using map-based sequencing and by Celera using shotgun sequencing. Shotgun sequencing is now the preferred method for other types of genome sequencing. The complete genomes of many organisms, such as the plant Arabidopsis thaliana, rice, cow, dog, chicken, chimpanzee, rat, mouse, puffer fish and many microorganisms have been sequenced in this way.
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