Genome project

Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus) and to annotate protein-coding genes and other important genome-encoded features. 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. Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus) and to annotate protein-coding genes and other important genome-encoded features. 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 was a landmark genome project that is already having a major impact on research across the life sciences, with potential for spurring numerous medical and commercial developments. Genome assembly refers to the process of taking a large number of short DNA sequences and putting them back together to create a representation of the original chromosomes from which the DNA originated. In a shotgun sequencing project, all the DNA from a source (usually a single organism, anything from a bacterium to a mammal) is first fractured into millions of small pieces. These pieces are then 'read' by automated sequencing machines, which can read up to 1000 nucleotides or bases at a time. (The four bases are adenine, guanine, cytosine, and thymine, represented as AGCT.) 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 some occur in thousands of 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'. 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 assembler Short Oligonucleotide Analysis Package developed by BGI for de novo assembly of human-sized genomes, alignment, SNP detection, resequencing, indel finding, and structural variation analysis. Since the 1980s, molecular biology and bioinformatics have created the need for DNA annotation. DNA annotation or genome annotation is the process of identifying attaching biological information to sequences, and particularly in identifying the locations of genes and determining what those genes do. When sequencing a genome, there are usually regions that are difficult to sequence (often regions with highly repetitive DNA). Thus, 'completed' genome sequences are rarely ever complete, and terms such as 'working draft' or 'essentially complete' have been used to more accurately describe the status of such genome projects. Even when every base pair of a genome sequence has been determined, there are still likely to be errors present because DNA sequencing is not a completely accurate process. It could also be argued that a complete genome project should include the sequences of mitochondria and (for plants) chloroplasts as these 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 genes in that particular genome sequence. The proportion of a genome that encodes for genes may be very small (particularly in eukaryotes such as humans, where coding DNA may only account for a few percent of the entire sequence). However, it is not always possible (or desirable) to only sequence the coding regions separately. Also, as scientists understand more about the role of this 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.