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An image of the faat making up the diploid genome of a human male. (The mitochondrial chromosome is not shown.)

In modern molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses). The genome includes both the genes (the coding regions) and the noncoding DNA,[1] as well as the genetic material of the mitochondria[2] and chloroplasts.

Contents

Origin of termEdit

The term genome was created in 1920 by Hans Winkler,[3] professor of botany at the University of Hamburg, Germany. The Oxford Dictionary suggests the name is a blend of the words gene and chromosome.[4] However, see omics for a more thorough discussion. A few related -ome words already existed—such as biome, rhizome, forming a vocabulary into which genome fits systematically.[5]

OverviewEdit

Some organisms have multiple copies of chromosomes: diploid, triploid, tetraploid and so on. In classical genetics, in a dumbass 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 diploid cell. The halving of the genetic material in gametes is accomplished by the segregation of homologous chromosomes during meiosis.[6] 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 or linear chains of DNA (or RNA for some viruses), likewise constitute the genome. The term genome can be applied specifically to mean what is stored on a complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to what is stored within organelles that contain their own DNA, as with the "mitochondrial genome" or the "chloroplast genome". Additionally, the genome can comprise non-chromosomal genetic elements such as viruses, plasmids, and transposable elements.[7]

Typically, when it is said that the genome of a sexually reproducing species has been "sequenced", it refers 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. Colloquially, the phrase "genetic makeup" is sometimes used to signify the genome of a particular individual or organism.[citation needed] 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 is 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.

The human genome is analogous to the instructions stored in a cookbook. Just as a cookbook gives the instructions needed to make a range of meals including a holiday feast or a summer picnic, the human genome contains all the instructions needed to make the full range of human cell types including muscle cells or neurons.

  • 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 contains approximately 20,000 different recipes (genes), which together make up less than 2% of the letters in the book.
  • The book fits into a cell nucleus the size of a pinpoint;
  • Most cells contain two copies of the book (all 23 chapters). Gametes (egg and sperm cells) contain only one copy, and mature red blood cells (which become enucleated during development) lack a genome.

Sequencing and mappingEdit

 
Part of DNA sequence - prototypification of complete genome of virus

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 next year Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs.[8] The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: The first bacterial genome to be sequenced 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 sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research.

The development of new technologies has made it dramatically easier and cheaper to do sequencing, and the number of complete genome sequences is growing rapidly. The US National Institutes of Health maintains one of several comprehensive databases of genomic information.[9] Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the puffer fish, and the bacteria E. coli. In December 2013, scientists first sequenced the entire genome of a Neanderthal, an extinct species of humans. The genome was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave.[10][11]

New sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine. A major step toward that goal was the completion in 2007 of the full genome of James D. Watson, one of the co-discoverers of the structure of DNA.[12]

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. The Human Genome Project was organized to map and to sequence the human genome. A fundamental step in the project was the release of a detailed genomic map by Jean Weissenbach and his team at the Genoscope in Paris.[13][14]

Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity.[15] The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service,[16] to the extent that one may submit one's genome to crowd sourced scientific endeavours such as DNA.land at the New York Genome Center, an example both of the economies of scale and of citizen science.[17]

Genome compositionEdit

Genome composition is used to describe the make up of a haploid genome, including the genome size and proportions of non-repetitive DNA and repetitive DNA. By comparing the genome compositions between genomes, scientists can better understand the evolutionary history of a given genome.

VirusesEdit

Viral genomes can be composed of either RNA or DNA. The genomes of RNA viruses can be either single-stranded or double-stranded RNA, and may contain one or more separate RNA molecules. DNA viruses can have either single-stranded or double-stranded genomes. Most DNA virus genomes are composed of a single, linear molecule of DNA, but some are made up of a circular DNA molecule.[18]

ProkaryotesEdit

Prokaryotes and eukaryotes have DNA genomes. Archaea have a single circular chromosome.[19] Most bacteria also have a single circular chromosome; however, some bacterial species have linear chromosomes[20] or multiple chromosomes.[21] If the DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell. Most prokaryotes have very little repetitive DNA in their genomes.[22]

Some bacteria have auxiliary genetic material, which is carried in plasmids.

EukaryotesEdit

Eukaryotic genomes are composed of one or more linear DNA chromosomes. The number of chromosomes varies widely from Jack jumper ants and an asexual nemotode,[23] which each have only one pair, to a fern species that has 720 pairs.[24] A typical human cell has two copies of each of 22 autosomes, one inherited from each parent, plus two sex chromosomes, making it diploid. Gametes, such as ova, sperm, spores, and pollen, are haploid, meaning they carry only one copy of each chromosome.

In addition to the chromosomes in the nucleus, organelles such as the chloroplasts and mitochondria have their own DNA. 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". Like the bacteria they originated from, mitochondria and chloroplasts have a circular chromosome.

Unlike prokaryotes, eukaryotes have exon-intron organization of protein coding genes and variable amounts of repetitive DNA. In mammals and plants, the majority of the genome is composed of repetitive DNA.[25]

Coding sequencesEdit

DNA sequences that carry the instructions to make proteins are coding sequences. The proportion of the genome occupied by coding sequences varies widely. A bigger genome does not mean more genes, and the proportion of non-repetitive DNA decreases along with increasing genome size in complex eukaryotes.[25]

Some E. coli only have non-repetitive DNA, simple eukaryotes such as C. elegans and fruit fly, possess more non-repetitive DNA than repetitive DNA.[25][26] Higher eukaryotes tend to have more repetitive DNA than non-repetitive ones.[27] In some plants and amphibians, the proportion of non-repetitive DNA is no more than 20%.[25] Only 2% of the human genome codes for proteins.

 
Composition of the human genome

Noncoding sequencesEdit

Noncoding sequences include introns, sequences for non-coding RNAs, regulatory regions, and repetitive DNA. Noncoding sequences make up 98% of the human genome. There are two categories of repetitive DNA in the genome: tandem repeats and interspersed repeats.[28]

Tandem repeatsEdit

Tandem repeats are short, non-coding sequences that are repeated head-to-tail. Microsatellites consist of 2-5 basepair repeats, while minisatellite repeats are 30-35 bp. Tandem repeats make up about 4% of the human genome and 9% of the fruit fly genome.[29] Telomeres are composed of the tandem repeat TTAGGG in mammals, and they play an important function in protecting the ends of the chromosome. Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion.[30]

Transposable elementsEdit

Transposable elements (TEs) are sequences of DNA with a defined structure that are able to change their location in the genome. [29][22][31] TEs are categorized as either class I TEs, which replicate by a copy-and-paste mechanism, or class II TEs, which can be excised from the genome and inserted at a new location.

The movement of TEs is a driving force of genome evolution in eukaryotes because their insertion can disrupt gene functions, homologous recombination between TEs can produce duplications, and TE can shuffle exons and regulatory sequences to new locations.[32]

RetrotransposonsEdit

Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome.[33] Retrotransposons can be divided into Long terminal repeats (LTRs) and Non-Long Terminal Repeats (Non-LTR).[32]

Long terminal repeats (LTRs) 
similar to retroviruses, which have both gag and pol genes to make cDNA from RNA and proteins to insert into genome, but LTRs can only act within the cell as they lack the env gene in retroviruses.[31] It has been reported that LTRs consist of the largest fraction in most plant genome and might account for the huge variation in genome size.[34]
Non-long terminal repeats (Non-LTRs) 
can be divided into long interspersed elements (LINEs), short interspersed elements (SINEs) and Penelope-like elements. In Dictyostelium discoideum, there is another DIRS-like elements belong to Non-LTRs. Non-LTRs are widely spread in eukaryotic genomes.[35]
Long interspersed elements (LINEs) 
are able to encode two Open Reading Frames (ORFs) to generate transcriptase and endonuclease, which are essential in retrotransposition. The human genome has around 500,000 LINEs, taking around 17% of the genome.[36]
Short interspersed elements (SINEs) 
are usually less than 500 base pairs and need to co-opt with the LINEs machinery to function as nonautonomous retrotransposons.[37] The Alu element is the most common SINEs found in primates, it has a length of about 350 base pairs and takes about 11% of the human genome with around 1,500,000 copies.[32]
DNA transposonsEdit

DNA transposons encode a transposase enzyme between inverted terminal repeats. When expressed, the transposase can catalyze the excision of the TE and its reinsertion in a new site.[29] This cut-and-paste mechanism typically reinserts transposons near their original location (within 100kb). [32] DNA transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm C. elegans.[32]

Genome sizeEdit

 
Log-log plot of the total number of annotated proteins in genomes submitted to GenBank as a function of genome size.[38]

Genome size is the total number of DNA base pairs in one copy of a haploid genome. In humans, the nuclear genome comprises approximately 3.2 billion nucleotides of DNA, divided into 24 linear molecules, the shortest 50 000 000 nucleotides in length and the longest 260 000 000 nucleotides, each contained in a different chromosome.[39] The genome size is positively correlated with the morphological complexity among prokaryotes and lower eukaryotes; however, after mollusks and all the other higher eukaryotes above, this correlation is no longer effective.[25][40] This phenomenon also indicates the mighty influence coming from repetitive DNA act on the genomes.

Since genomes 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 multi-cellular organisms (see Developmental biology). The work is both in vivo and in silico.[41][42]

Here is a table of some significant or representative genomes. See #See also for lists of sequenced genomes.

Organism type Organism Genome size
(base pairs)
Approx. no. of genes Note
Virus Porcine circovirus type 1 1,759 1.8kb Smallest viruses replicating autonomously in eukaryotic cells.[43]
Virus Bacteriophage MS2 3,569 3.5kb First sequenced RNA-genome[44]
Virus SV40 5,224 5.2kb [45]
Virus Phage Φ-X174 5,386 5.4kb First sequenced DNA-genome[46]
Virus HIV 9,749 9.7kb [47]
Virus Phage λ 48,502 48.5kb Often used as a vector for the cloning of recombinant DNA.

[48] [49] [50]

Virus Megavirus 1,259,197 1.3Mb Until 2013 the largest known viral genome.[51]
Virus Pandoravirus salinus 2,470,000 2.47Mb Largest known viral genome.[52]
Bacterium Nasuia deltocephalinicola (strain NAS-ALF) 112,091 112kb Smallest non-viral genome.[53]
Bacterium Carsonella ruddii 159,662 160kb
Bacterium Buchnera aphidicola 600,000 600kb [54]
Bacterium Wigglesworthia glossinidia 700,000 700Kb
Bacterium Haemophilus influenzae 1,830,000 1.8Mb First genome of a living organism sequenced, July 1995[55]
Bacterium Escherichia coli 4,600,000 4.6Mb 4288 [56]
Bacterium Solibacter usitatus (strain Ellin 6076) 9,970,000 10Mb [57]
Bacteriumcyanobacterium Prochlorococcus spp. (1.7 Mb) 1,700,000 1.7Mb 1884 Smallest known cyanobacterium genome[58][59]
Bacterium – cyanobacterium Nostoc punctiforme 9,000,000 9Mb 7432 7432 "open reading frames"[60]
Amoeboid Polychaos dubium ("Amoeba" dubia) 670,000,000,000 670Gb Largest known genome.[61] (Disputed)[62]
Eukaryotic organelle Human mitochondrion 16,569 16.6kb [63]
Plant Genlisea tuberosa 61,000,000 61Mb Smallest recorded flowering plant genome, 2014.[64]
Plant Arabidopsis thaliana 135,000,000 [65] 135 Mb 27,655[66] First plant genome sequenced, December 2000.[67]
Plant Populus trichocarpa 480,000,000 480Mb 73013 First tree genome sequenced, September 2006[68]
Plant Fritillaria assyrica 130,000,000,000 130Gb
Plant Paris japonica (Japanese-native, pale-petal) 150,000,000,000 150Gb Largest plant genome known[69]
Plant – moss Physcomitrella patens 480,000,000 480Mb First genome of a bryophyte sequenced, January 2008.[70]
Fungusyeast Saccharomyces cerevisiae 12,100,000 12.1Mb 6294 First eukaryotic genome sequenced, 1996[71]
Fungus Aspergillus nidulans 30,000,000 30Mb 9541 [72]
Nematode Pratylenchus coffeae 20,000,000 20Mb [73] Smallest animal genome known[74]
Nematode Caenorhabditis elegans 100,300,000 100Mb 19000 First multicellular animal genome sequenced, December 1998[75]
Insect Drosophila melanogaster (fruit fly) 175,000,000 175Mb 13600 Size variation based on strain (175-180Mb; standard y w strain is 175Mb)[76]
Insect Apis mellifera (honey bee) 236,000,000 236Mb 10157 [77])
Insect Bombyx mori (silk moth) 432,000,000 432Mb 14623 14,623 predicted genes[78]
Insect Solenopsis invicta (fire ant) 480,000,000 480Mb 16569 [79]
Mammal Mus musculus 2,700,000,000 2.7Gb 20210 [80]
Mammal Homo sapiens 3,289,000,000 3.3Gb 20000 Homo sapiens estimated genome size 3.2 billion bp[81]

Initial sequencing and analysis of the human genome[82]

Mammal Pan paniscus 3,286,640,000 3.3Gb 20000 Bonobo - estimated genome size 3.29 billion bp[83]
Fish Tetraodon nigroviridis (type of puffer fish) 385,000,000 390Mb Smallest vertebrate genome known estimated to be 340 Mb[84][85] – 385 Mb.[86]
Fish Protopterus aethiopicus (marbled lungfish) 130,000,000,000 130Gb Largest vertebrate genome known

Genome compressionEdit

Genomes are compressed according to reference-free and reference compression. See Hosseini et al. for a review on genome compression tools.[87]

Reference-free compressionEdit

The human reference genome (GRC v38) has been successfully compressed to ~5.2-fold (marginal less than 550 MB) in 155 minutes using a desktop computer with 6.4 GB of RAM.[88]

Reference compressionEdit

The compression ratio of currently available genomic data compression tools ranges between 65-fold and 1,200-fold for human genomes.[89][90][91][92][93][94][88]

Genomic alterationsEdit

All the cells of an organism originate from a single cell, so they are expected to have identical genomes; however, in some cases, differences arise. Both the process of copying DNA during cell division and exposure to environmental mutagens can result in mutations in somatic cells. In some cases, such mutations lead to cancer because they cause cells to divide more quickly and invade surrounding tissues.[95] In certain lymphocytes in the human immune system, V(D)J recombination generates different genomic sequences such that each cell produces a unique antibody or T cell receptors.

During meiosis, diploid cells divide twice to produce haploid germ cells. During this process, recombination results in a reshuffling of the genetic material from homologous chromosomes so each gamete has a unique genome.

Genome evolutionEdit

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 karyotype (chromosome number), 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. Duplication may range from extension of short tandem repeats, to duplication of a cluster of genes, and all the way to duplication 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 an 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. Recent empirical data suggest an important role of viruses and sub-viral RNA-networks to represent a main driving role to generate genetic novelty and natural genome editing.[96]

See alsoEdit

ReferencesEdit

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Further readingEdit

  • Benfey, P.; Protopapas, A.D. (2004). Essentials of Genomics. Prentice Hall. 
  • Brown, Terence A. (2002). Genomes 2. Oxford: Bios Scientific Publishers. ISBN 978-1-85996-029-5. 
  • Gibson, Greg; Muse, Spencer V. (2004). A Primer of Genome Science (Second ed.). Sunderland, Mass: Sinauer Assoc. ISBN 0-87893-234-8. 
  • Gregory (2005). T. Ryan, ed. The Evolution of the Genome. Elsevier. ISBN 0-12-301463-8. 
  • Reece, Richard J. (2004). Analysis of Genes and Genomes. Chichester: John Wiley & Sons. ISBN 0-470-84379-9. 
  • Saccone, Cecilia; Pesole, Graziano (2003). Handbook of Comparative Genomics. Chichester: John Wiley & Sons. ISBN 0-471-39128-X. 
  • Werner, E. (2003). "In silico multicellular systems biology and minimal genomes". Drug Discov Today. 8 (24): 1121–1127. doi:10.1016/S1359-6446(03)02918-0. PMID 14678738. 

External linksEdit