Genome project

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When printed, the human genome sequence fills around 100 huge books of close print

Genome projects are

bacterium, an archaean, a protist or a virus) and to annotate protein-coding genes and other important genome-encoded features.[1] The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes
and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences.

The Human Genome Project is a well known example of a genome project.[2]

Genome assembly

Main article: Sequence assembly

Genome assembly refers to the process of taking a large number of short

bacterium to a mammal) is first fractured into millions of small pieces. These pieces are then "read" by automated sequencing machines. A genome assembly algorithm
works by taking all the pieces and aligning them to one another, and detecting all places where two of the short sequences, or reads, overlap. These overlapping reads can be merged, and the process continues.

Genome assembly is a very difficult computational problem, made more difficult because many genomes contain large numbers of identical sequences, known as repeats. These repeats can be thousands of nucleotides long, and occur different locations, especially in the large genomes of plants and animals.

The resulting (draft) genome sequence is produced by combining the information sequenced contigs and then employing linking information to create scaffolds. Scaffolds are positioned along the physical map of the chromosomes creating a "golden path".

Assembly software

Originally, most large-scale DNA sequencing centers developed their own software for assembling the sequences that they produced. However, this has changed as the software has grown more complex and as the number of sequencing centers has increased. An example of such

BGI for de novo assembly of human-sized genomes, alignment, SNP detection, resequencing, indel finding, and structural variation analysis.[3][4][5]

Genome annotation

Main article: DNA annotation

Since the 1980s,

sequences
, and particularly in identifying the locations of genes and determining what those genes do.

Time of completion

When

organelles
have their own genomes.

It is often reported that the goal of sequencing a genome is to obtain information about the complete set of

noncoding DNA (often referred to as junk DNA
), it will become more important to have a complete genome sequence as a background to understanding the genetics and biology of any given organism.

In many ways genome projects do not confine themselves to only determining a DNA sequence of an organism. Such projects may also include

mRNAs
to help find out where the genes actually are.

Historical and technological perspectives

Historically, when sequencing eukaryotic genomes (such as the worm

shotgun sequenced
' in one go (there are caveats to this approach though when compared to the traditional approach).

Improvements in DNA sequencing technology has meant that the cost of sequencing a new genome sequence has steadily fallen (in terms of cost per base pair) and newer technology has also meant that genomes can be sequenced far more quickly.

When research agencies decide what new genomes to sequence, the emphasis has been on species which are either high importance as

common chimpanzee
).

In the future, it is likely that it will become even cheaper and quicker to sequence a genome. This will allow for complete genome sequences to be determined from many different individuals of the same species. For humans, this will allow us to better understand aspects of human genetic diversity.

Examples

Main articles:
List of sequenced prokaryotic genomes
Bovine Genome Project
The Giant Sequoia genome sequence was extracted from a single fertilized seed harvested from a 1,360-year-old tree in Sequoia/Kings Canyon National Park.

Many organisms have genome projects that have either been completed or will be completed shortly, including:

See also

References

  1. ISBN 9780470085851
    .
  2. ^ "Potential Benefits of Human Genome Project Research". Department of Energy, Human Genome Project Information. 2009-10-09. Archived from the original on 2013-07-08. Retrieved 2010-06-18.
  3. PMID 20019144
    .
  4. ^
    PMID 20148029
    .
  5. PMID 18987735
    .
  6. ^ Ghosh, Pallab (23 April 2015). "Mammoth genome sequence completed". BBC News.
  7. ^ Yates, Diana (2009-04-23). "What makes a cow a cow? Genome sequence sheds light on ruminant evolution" (Press Release). EurekAlert!. Retrieved 2012-12-22.
  8. PMID 19390049
    .
  9. ^ "2007 Release: Horse Genome Assembled". National Human Genome Research Institute (NHGRI). Retrieved 19 April 2018.
  10. PMID 32948606
    .

External links

The Wikibook Next Generation Sequencing (NGS) has a page on the topic of: De_novo_assembly
Wikimedia Commons has media related to Genome projects.
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