In the fields of molecular biology and genetics, a genome is all the genetic information of an

organism.[1] It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear
genome includes protein-coding genes and non-coding genes, other functional regions of the
genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction
of junk DNA with no evident function.[2][3] Almost all eukaryotes have mitochondria and a
small mitochondrial genome.[2] Algae and plants also contain chloroplasts with a chloroplast genome.
The study of the genome is called genomics. The genomes of many organisms have been
sequenced and various regions have been annotated. The Human Genome Project was started in
October 1990, and then reported the sequence of the human genome in April 2003,[4] although the
initial "finished" sequence was missing 8% of the genome consisting mostly of repetitive sequences.
[5]

With advancements in technology that could handle sequencing of the many repetitive sequences
found in human DNA that were not fully uncovered by the original Human Genome Project study,
scientists reported the first end-to-end human genome sequence in March 2022.[6]

Origin of the term[edit]

Look up genome in Wiktionary, the free dictionary.

The term genome was created in 1920 by Hans Winkler,[7] professor of botany at the University of
Hamburg, Germany. The website Oxford Dictionaries and the Online Etymology Dictionary suggest
the name is a blend of the words gene and chromosome.[8][9][10][11] However, see omics for a more
thorough discussion. A few related -ome words already existed, such as biome and rhizome, forming
a vocabulary into which genome fits systematically.[12]

Definition[edit]
It's very difficult to come up with a precise definition of "genome." It usually refers to the DNA (or
sometimes RNA) molecules that carry the genetic information in an organism but sometimes it is
difficult to decide which molecules to include in the definition; for example, bacteria usually have one
or two large DNA molecules (chromosomes) that contain all of the essential genetic material but they
also contain smaller extrachromosomal plasmid molecules that carry important genetic information.
The definition of 'genome' that's commonly used in the scientific literature is usually restricted to the
large chromosomal DNA molecules in bacteria.[13]
Eukaryotic genomes are even more difficult to define because almost all eukaryotic species contain
nuclear chromosomes plus extra DNA molecules in the mitochondria. In addition, algae and plants
have chloroplast DNA. Most textbooks make a distinction between the nuclear genome and the
organelle (mitochondria and chloroplast) genomes so when they speak of, say, the human genome,
they are only referring to the genetic material in the nucleus.[2][14] This is the most common use of
'genome' in the scientific literature.
Most eukaryotes are diploid, meaning that there are two copies of each chromosome in the nucleus
but the 'genome' refers to only one copy of each chromosome. Some eukaryotes have distinctive
sex chromosomes such as the X and Y chromosomes of mammals so the technical definition of the
genome must include both copies of the sex chromosomes. When referring to the standard
reference genome of humans, for example, it consists of one copy of each of the 22 autosomes plus
one X chromosome and one Y chromosome.[15]
Sequencing and mapping[edit]
Further information: Genome project
A genome sequence is the complete list of the nucleotides (A, C, G, and T for DNA genomes) that
make up all the chromosomes of an individual or a species. Within a species, the vast majority of
nucleotides are identical between individuals, but sequencing multiple individuals is necessary to
understand the genetic diversity.

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.[16] 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.[citation needed]
The development of new technologies has made genome sequencing dramatically cheaper and
easier, 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.
[17]
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.[18][19]
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.[20]
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.[21][22]
Reference genome sequences and maps continue to be updated, removing errors and clarifying
regions of high allelic complexity.[23] The decreasing cost of genomic mapping has
permitted genealogical sites to offer it as a service,[24] to the extent that one may submit one's
genome to crowdsourced scientific endeavours such as DNA.LAND at the New York Genome
Center,[25] an example both of the economies of scale and of citizen science.[26]

Viral genomes[edit]
Viral genomes can be composed of either RNA or DNA. The genomes of RNA viruses can be
either single-stranded RNA or double-stranded RNA, and may contain one or more separate RNA
molecules (segments: monopartit or multipartit genome). 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.[27]

Prokaryotic genomes[edit]
Prokaryotes and eukaryotes have DNA genomes. Archaea and most bacteria have a single circular
chromosome,[28] however, some bacterial species have linear or multiple chromosomes.[29][30] If the
DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be
present in a single cell, and if the cells divide faster than the DNA can be replicated, multiple
replication of the chromosome is initiated before the division occurs, allowing daughter cells to inherit
complete genomes and already partially replicated chromosomes. Most prokaryotes have very little
repetitive DNA in their genomes.[31] However, some symbiotic bacteria (e.g. Serratia symbiotica) have
reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins. [32]
[33]

Some bacteria have auxiliary genetic material, also part of their genome, which is carried
in plasmids. For this, the word genome should not be used as a synonym of chromosome.

Eukaryotic genomes[edit]
See also: Eukaryotic chromosome fine structure
In a typical human cell, the genome is contained in 22 pairs of autosomes, two sex chromosomes (the female
and male variants shown at bottom right), as well as the mitochondrial genome (shown to scale as "MT" at
bottom left).
Further information: Karyotype

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,[34] which each have
only one pair, to a fern species that has 720 pairs.[35] It is surprising the amount of DNA that
eukaryotic genomes contain compared to other genomes. The amount is even more than what is
necessary for DNA protein-coding and noncoding genes due to the fact that eukaryotic genomes
show as much as 64,000-fold variation in their sizes.[36] However, this special characteristic is caused
by the presence of repetitive DNA, and transposable elements (TEs).
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 where exon-intron organization of protein coding genes exists but is rather
exceptional, eukaryotes generally have these features in their genes and their genomes contain
variable amounts of repetitive DNA. In mammals and plants, the majority of the genome is
composed of repetitive DNA.[37] Genes in eukaryotic genomes can be annotated using FINDER.[38] [39]

DNA sequencing[edit]
High-throughput technology makes sequencing to assemble new genomes accessible to everyone.
Sequence polymorphisms are typically discovered by comparing resequenced isolates to a
reference, whereas analyses of coverage depth and mapping topology can provide details regarding
structural variations such as chromosomal translocations and segmental duplications.

Coding sequences[edit]
DNA sequences that carry the instructions to make proteins are referred to as coding sequences.
The proportion of the genome occupied by coding sequences varies widely. A larger genome does
not necessarily contain more genes, and the proportion of non-repetitive DNA decreases along with
increasing genome size in complex eukaryotes.[37]

Composition of the human genome

Noncoding sequences[edit]
Main article: Non-coding DNA
See also: Intergenic region
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.[40]
Tandem repeats[edit]
Short, non-coding sequences that are repeated head-to-tail are called tandem repeats.
Microsatellites consisting 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. [41] Tandem repeats
can be functional. For example, telomeres are composed of the tandem repeat TTAGGG in
mammals, and they play an important role in protecting the ends of the chromosome.
In other cases, expansions in the number of tandem repeats in exons or introns can cause disease.
[42]
For example, the human gene huntingtin (Htt) typically contains 6–29 tandem repeats of the
nucleotides CAG (encoding a polyglutamine tract). An expansion to over 36 repeats results
in Huntington's disease, a neurodegenerative disease. Twenty human disorders are known to result
from similar tandem repeat expansions in various genes. The mechanism by which proteins with
expanded polygulatamine tracts cause death of neurons is not fully understood. One possibility is
that the proteins fail to fold properly and avoid degradation, instead accumulating in aggregates that
also sequester important transcription factors, thereby altering gene expression. [42]
Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene
conversion.[43]
Transposable elements[edit]
Transposable elements (TEs) are sequences of DNA with a defined structure that are able to
change their location in the genome.[41][31][44] TEs are categorized as either as a mechanism that
replicates by copy-and-paste or as a mechanism that can be excised from the genome and inserted
at a new location. In the human genome, there are three important classes of TEs that make up
more than 45% of the human DNA; these classes are The long interspersed nuclear elements
(LINEs), The interspersed nuclear elements (SINEs), and endogenous retroviruses. These elements
have a big potential to modify the genetic control in a host organism.[36]
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.[45]
Retrotransposons[edit]
Retrotransposons[46] are found mostly in eukaryotes but not found in prokaryotes and
retrotransposons form a large portion of genomes of many eukaryotes. Retrotransposon is a
transposable element that transpose through an RNA intermediate. Retrotransposons[47] are
composed of DNA, but are transcribed into RNA for transposition, then the RNA transcript is copied
back to DNA formation with the help of a specific enzyme called reverse transcriptase.
Retrotransposons that carry reverse transcriptase in their gene can trigger its own transposition but
the genes that lack the reverse transcriptase must use reverse transcriptase synthesized by another
retrotransposon. Retrotransposons can be transcribed into RNA, which are then duplicated at
another site into the genome.[48] Retrotransposons can be divided into long terminal repeats (LTRs)
and non-long terminal repeats (Non-LTRs).[45]
Long terminal repeats (LTRs) are derived from ancient retroviral infections, so they encode
proteins related to retroviral proteins including gag (structural proteins of the virus), pol (reverse
transcriptase and integrase), pro (protease), and in some cases env (envelope) genes. [44] These
genes are flanked by long repeats at both 5' and 3' ends. 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. [49]
Non-long terminal repeats (Non-LTRs) are classified as long interspersed nuclear
elements (LINEs), short interspersed nuclear elements (SINEs), and Penelope-like elements (PLEs).
In Dictyostelium discoideum, there is another DIRS-like elements belong to Non-LTRs. Non-LTRs
are widely spread in eukaryotic genomes.[50]
Long interspersed elements (LINEs) encode genes for reverse transcriptase and endonuclease,
making them autonomous transposable elements. The human genome has around 500,000 LINEs,
taking around 17% of the genome.[51]
Short interspersed elements (SINEs) are usually less than 500 base pairs and are non-autonomous,
so they rely on the proteins encoded by LINEs for transposition.[52] The Alu element is the most
common SINE found in primates. It is about 350 base pairs and occupies about 11% of the human
genome with around 1,500,000 copies.[45]
DNA transposons[edit]
DNA transposons encode a transposase enzyme between inverted terminal repeats. When
expressed, the transposase recognizes the terminal inverted repeats that flank the transposon and
catalyzes its excision and reinsertion in a new site.[41] This cut-and-paste mechanism typically
reinserts transposons near their original location (within 100kb).[45] DNA transposons are found in
bacteria and make up 3% of the human genome and 12% of the genome of the roundworm C.
elegans.[45]

Genome size[edit]
Log–log plot of the total number of annotated proteins in genomes submitted to GenBank as a function of
genome size

Genome size is the total number of the DNA base pairs in one copy of a haploid genome. Genome
size varies widely across species. Invertebrates have small genomes, this is also correlated to a
small number of transposable elements. Fish and Amphibians have intermediate-size genomes, and
birds have relatively small genomes but it has been suggested that birds lost a substantial portion of
their genomes during the phase of transition to flight. Before this loss, DNA methylation allows the
adequate expansion of the genome.[36]
In humans, the nuclear genome comprises approximately 3.1 billion nucleotides of DNA, divided into
24 linear molecules, the shortest 45 000 000 nucleotides in length and the longest 248 000 000
nucleotides, each contained in a different chromosome.[53] There is no clear and consistent
correlation between morphological complexity and genome size in either prokaryotes or
lower eukaryotes.[37][54] Genome size is largely a function of the expansion and contraction of
repetitive DNA elements.
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.[55][56]

Genome size differences due to transposable elements[edit]

Comparison among genome sizes

There are many enormous differences in size in genomes, specially mentioned before in the
multicellular eukaryotic genomes. Much of this is due to the differing abundances of transposable
elements, which evolve by creating new copies of themselves in the chromosomes. [36] Eukaryote
genomes often contain many thousands of copies of these elements, most of which have acquired
mutations that make them defective. Here is a table of some significant or representative genomes.
See #See also for lists of sequenced genomes.