page_title: Genomic library
section_title: Hierarchical sequencing
hierarchical_section_title: Genomic library / Applications / Hierarchical sequencing
caption_attribution_description: English: In whole genome shotgun sequencing (top), the entire genome is sheared randomly into small fragments (appropriately sized for sequencing) and then reassembled. In hierarchical shotgun sequencing (bottom), the genome is first broken into larger segments. After the order of these segments is deduced, they are further sheared into fragments appropriately sized for sequencing.
context_page_description: A genomic library is a collection of the total genomic DNA from a single organism. The DNA is stored in a population of identical vectors, each containing a different insert of DNA. In order to construct a genomic library, the organism's DNA is extracted from cells and then digested with a restriction enzyme to cut the DNA into fragments of a specific size. The fragments are then inserted into the vector using DNA ligase. Next, the vector DNA can be taken up by a host organism - commonly a population of Escherichia coli or yeast - with each cell containing only one vector molecule. Using a host cell to carry the vector allows for easy amplification and retrieval of specific clones from the library for analysis.
  There are several kinds of vectors available with various insert capacities. Generally, libraries made from organisms with larger genomes require vectors featuring larger inserts, thereby fewer vector molecules are needed to make the library. Researchers can choose a vector also considering the ideal insert size to find the desired number of clones necessary for full genome coverage.
  Genomic libraries are commonly used for sequencing applications.
context_section_description: One major use of genomic libraries is hierarchichal shotgun sequencing, which is also called top-down, map-based or clone-by-clone sequencing. This strategy was developed in the 1980s for sequencing whole genomes before high throughput techniques for sequencing were available. Individual clones from genomic libraries can be sheared into smaller fragments, usually 500bp to 1000bp, which are more manageable for sequencing. Once a clone from a genomic library is sequenced, the sequence can be used to screen the library for other clones containing inserts which overlap with the sequenced clone. Any new overlapping clones can then be sequenced forming a contig. This technique, called chromosome walking, can be exploited to sequence entire chromosomes.
  Whole genome shotgun sequencing is another method of genome sequencing that does not require a library of high-capacity vectors. Rather, it uses computer algorithms to assemble short sequence reads to cover the entire genome. Genomic libraries are often used in combination with whole genome shotgun sequencing for this reason. A high resolution map can be created by sequencing both ends of inserts from several clones in a genomic library. This map provides sequences of known distances apart, which can be used to help with the assembly of sequence reads acquired through shotgun sequencing. The human genome sequence, which was declared complete in 2003, was assembled using both a BAC library and shotgun sequencing.
caption: Whole genome shotgun sequencing versus Hierarchical shotgun sequencing
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