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Genome
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In classical genetics, the genome of a diploid organism including eukarya refers to a full set of chromosomes or genes in a gamete; thereby, a regular somatic cell contains two full sets of genomes. In a haploid organism, including bacteria, archaea, virus, and mitochondria, a cell contains only a single set of genome, usually in a single circular or contiguous linear DNA (or RNA for some viruses). In modern molecular biology the genome of an organism is its hereditary information encoded in DNA (or, for some viruses, RNA).
The genome includes both the genes and the non-coding sequences of the DNA.
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In classical genetics, the genome of a diploid organism including eukarya refers to a full set of chromosomes or genes in a gamete; thereby, a regular somatic cell contains two full sets of genomes. In a haploid organism, including bacteria, archaea, virus, and mitochondria, a cell contains only a single set of genome, usually in a single circular or contiguous linear DNA (or RNA for some viruses). In modern molecular biology the genome of an organism is its hereditary information encoded in DNA (or, for some viruses, RNA).
The genome includes both the genes and the non-coding sequences of the DNA. The term was adapted in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany. The Oxford English Dictionary suggests the name to be a portmanteau of the words gene and chromosome, however, many related -ome words already existed, such as biome and rhizome, forming a vocabulary into which genome fits systematically.
More precisely, the genome of an organism is a complete genetic sequence on one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell. The term genome can be applied specifically to mean that stored on a complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to that stored within organelles that contain their own DNA, as with the mitochondrial genome or the chloroplast genome. Additionally, the genome can comprise nonchromosomal genetic elements such as viruses, plasmids, and transposable elements. When people say that the genome of a sexually reproducing species has been "sequenced", typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as "a genome sequence" may be a composite read from the chromosomes of various individuals. In general use, the phrase "genetic makeup" is sometimes used conversationally to mean the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.
Both the number of base pairs and the number of genes vary widely from one species to another, and there is little connection between the two (an observation known as the C-value paradox). At present, the highest known number of genes is around 60,000, for the protozoan causing trichomoniasis (see List of sequenced eukaryotic genomes), almost three times as many as in the human genome.
An analogy to the human genome stored on DNA is that of instructions stored in a book:
- The book is over one billion words long;
- The book is bound 5000 volumes, each 300 pages long;
- The book fits into a cell nucleus the size of a pinpoint;
- A copy of the book (all 5000 volumes) is contained in almost every cell;
Types
Most biological entities that are more complex than a virus sometimes or always carry additional genetic material besides that which resides in their chromosomes. 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. In such circumstances then, "genome" describes all of the genes and information on non-coding DNA that have the potential to be present.
In eukaryotes such as plants, protozoa and animals, however, "genome" carries the typical connotation of only information on chromosomal DNA. So although these organisms contain mitochondria that have their own DNA, the genes in this mitochondrial DNA are not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome, often referred to as the "mitochondrial genome".
Genomes and genetic variation
Note that a genome does not capture the genetic diversity or the genetic polymorphism of a species. For example, the human genome sequence in principle could be determined from just half the information on the DNA of one cell from one individual. To learn what variations in genetic information underlie particular traits or diseases requires comparisons across individuals. This point explains the common usage of "genome" (which parallels a common usage of "gene") to refer not to the information in any particular DNA sequence, but to a whole family of sequences that share a biological context.
Although this concept may seem counter intuitive, it is the same concept that says there is no particular shape that is the shape of a cheetah. Cheetahs vary, and so do the sequences of their genomes. Yet both the individual animals and their sequences share commonalities, so one can learn something about cheetahs and "cheetah-ness" from a single example of either.
Sequencing and mapping
The Human Genome Project was organized to map and to sequence the human genome. Other genome projects include mouse, rice, the plant Arabidopsis thaliana, the puffer fish, bacteria like E. coli, etc. In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome (bacteriophage MS2). The first DNA-genome project to be completed was the Phage F-X174, with only 5368 base pairs, which was sequenced by Fred Sanger in 1977 . The first bacterial genome to be completed was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995.
The development of new technologies has dramatically decreased the difficulty and cost of sequencing, and the number of complete genome sequences is rising rapidly. Among many genome database sites, the one maintained by the US National Institutes of Health is inclusive.
These new technologies open up the prospect of personal genome sequencing as an important diagnostic tool. A major step toward that goal was the May 2007 New York Times announcement that the full genome of DNA pioneer James D. Watson was deciphered.
Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than a genome sequence and aids in navigating around the genome.
Comparison of different genome sizes
| Organism type | Organism | Genome size (base pairs)
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| Virus | Bacteriophage MS2 | 3,569 | First sequenced RNA-genome | | Virus | SV40 | 5,224 | | | Virus | Phage F-X174 | 5,386 | First sequenced DNA-genome | | Virus | Phage ? | 48,502 | | | Bacterium | Haemophilus influenzae | 1,830,000 | First genome of living organism, July 1995 | | Bacterium | Carsonella ruddii | 160,000 | Smallest non-viral genome. | | Bacterium | Buchnera aphidicola | 600,000 | | | Bacterium | Wigglesworthia glossinidia | 700,000 | | | Bacterium | Escherichia coli | 4,600,000 | | | Amoeba | Amoeba dubia | 670,000,000,000 | Largest known genome. | | Plant | Arabidopsis thaliana | 157,000,000 | First plant genome sequenced, Dec 2000. | | Plant | Genlisea margaretae | 63,400,000 | Smallest recorded flowering plant genome, 2006. | | Plant | Fritillaria assyrica | 130,000,000,000 | | | Plant | Populus trichocarpa | 480,000,000 | First tree genome, Sept 2006 | | Moss | Physcomitrella patens | 480,000,000 | First genome of a bryophyte, January 2008 | | Yeast | Saccharomyces cerevisiae | 12,100,000 | | | Fungus | Aspergillus nidulans | 30,000,000 | | | Nematode | Caenorhabditis elegans | 98,000,000 | First multicellular animal genome, December 1998 | | Insect | Drosophila melanogaster (fruit fly) | 130,000,000 | | | Insect | Bombyx mori (silk moth) | 530,000,000 | | | Insect | Apis mellifera (honey bee) | 1,770,000,000 | | | Fish | Tetraodon nigroviridis (type of puffer fish) | 385,000,000 | Smallest vertebrate genome known | | Mammal | Homo sapiens | 3,200,000,000 | | | Fish | Protopterus aethiopicus (marbled lungfish) | 130,000,000,000 | Largest vertebrate genome known |
Note: The DNA from a single human cell has a length of ~1.8 m (but at a width of ~2.4 nanometers).
Since genomes and their organisms are very complex, one research strategy is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multicellular organisms (see Developmental biology). The work is both in vivo and in silico.
Genome evolution
Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to the details of any particular genes and their products. Researchers compare traits such as chromosome number (karyotype), genome size, gene order, codon usage bias, and GC-content to determine what mechanisms could have produced the great variety of genomes that exist today (for recent overviews, see Brown 2002; Saccone and Pesole 2003; Benfey and Protopapas 2004; Gibson and Muse 2004; Reese 2004; Gregory 2005).
Duplications play a major role in shaping the genome. Duplications may range from extension of short tandem repeats, to duplication of a cluster of genes, and all the way to duplications of entire chromosomes or even entire genomes. Such duplications are probably fundamental to the creation of genetic novelty.
Horizontal gene transfer is invoked to explain how there is often extreme similarity between small portions of the genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes. Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes.
See also
Further reading
External links
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- [https://www.crops.org/genome/ The Plant Genome]
- The Integrated Microbial Genomes system, for genome analysis by the DOE-JGI.
- Cyberinfrastructure for Metagenomics, data repository and bioinformatics tools for metagenomic research
- an integrated database of human genes.
- - lecture by Sydney Brenner
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