genome sequencing

(noun)

a laboratory process that determines the complete DNA sequence of an organism's genome at a single time

Related Terms

Examples of genome sequencing in the following topics:

  • Uses of Genome Sequences

    • Genome sequences and expression can be analyzed using DNA microarrays, which can contribute to detection of disease and genetic disorders.
    • Almost one million genotypic abnormalities can be discovered using microarrays, whereas whole-genome sequencing can provide information about all six billion base pairs in the human genome.
    • Although the study of medical applications of genome sequencing is interesting, this discipline tends to dwell on abnormal gene function.
    • Genomics is still in its infancy, although someday it may become routine to use whole-genome sequencing to screen every newborn to detect genetic abnormalities.
    • It sounds great to have all the knowledge we can get from whole-genome sequencing; however, humans have a responsibility to use this knowledge wisely.

  • Use of Whole-Genome Sequences of Model Organisms

    • The first genome to be completely sequenced was of a bacterial virus, the bacteriophage fx174 (5368 base pairs).
    • Several other organelle and viral genomes were later sequenced.
    • It took this long because it was 60 times bigger than any other genome that had been sequenced at that point.
    • Having entire genomes sequenced aids these research efforts.
    • The process of attaching biological information to gene sequences is called genome annotation.

  • Annotating Genomes

    • Genome annotation is the identification and understanding of the genetic elements of a sequenced genome.
    • The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism.
    • Once a genome is sequenced, it needs to be annotated to make sense of it.
    • Genome annotation is the process of attaching biological information to sequences.
    • Genome annotation is the next major challenge for the Human Genome Project, now that the genome sequences of human and several model organisms are largely complete.

  • DNA Sequencing Techniques

    • Next generation sequencing can sequence a comparably-sized genome in a matter of days, using a single machine, at a cost of under $10,000.
    • Many researchers have set a goal of improving sequencing methods even more until a single human genome can be sequenced for under $1000.
    • Most genomic sequencing projects today make use of an approach called whole genome shotgun sequencing.
    • Whole genome shotgun sequencing involves isolating many copies of the chromosomal DNA of interest.
    • Genome sequencing will greatly advance our understanding of genetic biology.

  • Strategies Used in Sequencing Projects

    • The strategies used for sequencing genomes include the Sanger method, shotgun sequencing, pairwise end, and next-generation sequencing.
    • All of the segments are then sequenced using the chain-sequencing method.
    • This was sufficient for sequencing small genomes.
    • However, the desire to sequence larger genomes, such as that of a human, led to the development of double-barrel shotgun sequencing, more formally known as pairwise-end sequencing.
    • Compare the different strategies used for whole-genome sequencing:  Sanger method, shotgun sequencing, pairwise-end sequencing, and next-generation sequencing

  • Whole-Genome DNA-Binding Analysis

    • Whole-genome DNA-binding analysis is a powerful tool for analyzing epigenetic modifications and DNA sequences bound to regulatory proteins.
    • Genomic DNA sequences are being determined at an increasingly rapid pace.
    • A whole-genome approach was established to identify and characterize such DNA sequences.
    • The method of chromatin immunoprecipitation, combined with microarrays (ChIP-Chip), is a powerful tool for genome-wide analysis of protein binding.
    • It has also become a widely-used method for genome-wide localization of protein-DNA interactions.

  • DNA Sequencing of Insertion Sites

    • Although insertion sequences are usually discussed in the context of prokaryotic genomes, certain eukaryotic DNA sequences belonging to the family of Tc1/mariner transposable elements may be considered to be insertion sequences.
    • The resolvase is part of the tns genome and cuts at flanking inverted repeats.
    • These include Southern hybridization, inverse Polymerase Chain Reaction (iPCR), and most recently, vectorette PCR to identify and map the genomic positions of the insertion sequences.
    • However, when a target sequence has multiple genomic locations, the variously-sized DNA circles formed are difficult to amplify simultaneously.
    • It involves cutting genomic DNAs with a restriction enzyme, ligating vectorettes to the ends, and amplifying the flanking sequences of a known sequence using primers derived from the known sequence along with a vectorette primer.

  • Noncoding DNA

    • Noncoding DNA are sequences of DNA that do not encode protein sequences but can be transcribed to produce important regulatory molecules.
    • In genomics and related disciplines, noncoding DNA sequences are components of an organism's DNA that do not encode protein sequences.
    • For example, over 98% of the human genome is noncoding DNA, while only about 2% of a typical bacterial genome is noncoding DNA.
    • Other noncoding sequences have likely, but as-yet undetermined, functions.
    • More than 98% of the human genome does not encode protein sequences, including most sequences within introns and most intergenic DNA.

  • Physical Maps and Integration with Genetic Maps

    • The creation of genomic libraries and complementary DNA (cDNA) libraries (collections of cloned sequences or all DNA from a genome) has sped up the process of physical mapping.
    • A genetic site used to generate a physical map with sequencing technology (a sequence-tagged site, or STS) is a unique sequence in the genome with a known exact chromosomal location.
    • An expressed sequence tag (EST) and a single sequence length polymorphism (SSLP) are common STSs.
    • Information obtained from each technique is used in combination to study the genome.
    • Genomic mapping is being used with different model research organisms.

  • Bacterial Genomes

    • Bacterial genomes are smaller in size (size range from 139 kbp to 13,000 kpb) between species when compared with genomes of eukaryotes.
    • Recent advances in sequencing technology led to the discovery of a high correlation between the number of genes and the genome size of bacteria, suggesting that bacteria have relatively small amounts of junk DNA.
    • In some contexts, such as sequencing the genome of a pathogenic microbe, "genome" is meant to include information stored on this auxiliary material, which is carried in plasmids.
    • As such, selection can effectively operate on free-living bacteria to remove deleterious sequences resulting in a relatively small number of pseudogenes.
    • Unlike eukaryotes, bacteria show a strong correlation between genome size and number of functional genes in a genome.