Genome

In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA.

Origin of Term

The term was adapted in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany. In Greek, the word genome (γίνομαι) means "I become, I am born, to come into being". The Oxford English Dictionary suggests the name to be a blend of the words gene and chromosome. A few related -ome words already existed, such as biome and rhizome, forming a vocabulary into which genome fits systematically.

Overview

Some organisms have multiple copies of chromosomes, diploid, triploid, tetraploid and so on. In classical genetics, in a sexually reproducing organism (typically eukarya) the gamete has half the number of chromosomes of the somatic cell and the genome is a full set of chromosomes in a gamete. In haploid organisms, including cells of bacteria, archaea, and in organelles including mitochondria and chloroplasts, or viruses, that similarly contain genes, the single or set of circular and/or linear chains of DNA (or RNA for some viruses), likewise constitute the genome. 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 only a rough correlation 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 (genome) would contain 23 chapters (chromosomes);

each chapter contains 48 to 250 million letters (A,C,G,T) without spaces;

Hence, the book contains over 3.2 billion letters total;

The book fits into a cell nucleus the size of a pinpoint;

At least one copy of the book (all 23 chapters) is contained in most cells of our body. The only exception in humans is found in mature red blood cells which become enucleated during development and therefore lack a genome.

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 chloroplasts and/or mitochondria that have their own DNA, the genetic information contained by DNA within these organelles is not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome often referred to as the "mitochondrial genome". The DNA found within the chloroplast may be referred to as the "plastome".

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, and bacteria like E. coli. 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 Φ-X174, with only 5386 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. A few months later, the first eukaryotic genome was completed, with the 16 chromosomes of budding yeast Saccharomyces cerevisiae being released as a result of a European led effort initiated in the mid-80's.

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 completion of the decipherment of the full genome of DNA pioneer James D. Watson in 2007.

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. A fundamental step in the Human genome project was the release of a detailed genomic map by Jean Weissenbach and his team at the Genoscope in Paris

Comparison of different genome sizes

{| class="wikitable sortable" |- !Organism type !Organism !Genome size (base pairs) !mass - in pg !!class="unsortable" |Note |- |Virus |Bacteriophage MS2 |align="right"|3,569 |align="right"|0.000002 | First sequenced RNA-genome |- |Virus |SV40 |align="right"|5,224 | | |- |Virus |Phage Φ-X174 |align="right"|5,386 | |First sequenced DNA-genome |- |Virus |HIV |align="right"|9,749 | | |- |Virus |Phage λ |align="right"|48,502 | |- |Virus |Mimivirus |align="right"|1,181,404 | |Largest known viral genome |- |Bacterium |Haemophilus influenzae |align="right"| 1,830,000 | |First genome of a living organism sequenced, July 1995 |- |Bacterium |Carsonella ruddii |align="right"|159,662 | |Smallest non-viral genome. |- |Bacterium |Buchnera aphidicola |align="right"|600,000 | |- |Bacterium |Wigglesworthia glossinidia |align="right"|700,000 | |- |Bacterium |Escherichia coli |align="right"|4,600,000 | | |- |Bacterium |Solibacter usitatus (strain Ellin 6076) |align="right"|9,970,000 | |Largest known Bacterial genome |- |Amoeboid |Polychaos dubium ("Amoeba" dubia) |align="right"|670,000,000,000 |align="right"|737 |Largest known genome. (Disputed ) |- |Plant |Arabidopsis thaliana |align="right"|157,000,000 | |First plant genome sequenced, December 2000. |- |Plant |Genlisea margaretae |align="right"|63,400,000 | |Smallest recorded flowering plant genome, 2006. |- |Yeast |Saccharomyces cerevisiae |align="right"|12,100,000 | |First eukaryotic genome sequenced, 1996 |- |Fungus |Aspergillus nidulans |align="right"|30,000,000 | |- |Nematode |Caenorhabditis elegans |align="right"|100,300,000 | |First multicellular animal genome sequenced, December 1998 |- |Nematode |Pratylenchus coffeae |align="right"|20,000,000 | |Smallest animal genome known |- |Insect |Drosophila melanogaster (fruit fly) |align="right"|130,000,000 | | |- |Insect |Bombyx mori (silk moth) |align="right"|530,000,000 | |- |Insect |Apis mellifera (honey bee) |align="right"|236,000,000 | |- |Insect |Solenopsis invicta (fire ant) |align="right"|480,000,000 | | |- |Fish |Tetraodon nigroviridis (type of puffer fish) |align="right"|385,000,000 | |Smallest vertebrate genome known |- |Mammal |Homo sapiens |align="right"|3,200,000,000 |align="right"|3 | |- |Fish |Protopterus aethiopicus (marbled lungfish) |align="right"|130,000,000,000 |align="right"|143 |Largest vertebrate genome known |}

Note: The DNA from a single (diploid) human cell if the 46 chromosomes were connected end-to-end and straightened, would have a length of ~2 m and 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

Full genome sequencing

References

Further reading

External links

Build a DNA Molecule

Some comparative genome sizes

DNA Interactive: The History of DNA Science

DNA From The Beginning

All About The Human Genome Project — from Genome.gov

Animal genome size database

Plant genome size database

GOLD:Genomes OnLine Database

The Genome News Network

NCBI Entrez Genome Project database

NCBI Genome Primer

GeneCards — an integrated database of human genes

BBC News - Final genome 'chapter' published

IMG (The Integrated Microbial Genomes system) — for genome analysis by the DOE-JGI

GeKnome Technologies Next-Gen Sequencing Data Analysis — next-generation sequencing data analysis for Illumina and 454 Service from GeKnome Technologies.

Category:Genetic mapping Category:Genomics