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Genome
The hereditary (the passing of traits from parents to their offspring, either through asexual
reproduction or sexual reproduction) nature of every living organism is defined by its genome.
The term genome refers to all of the genetic material in an organism. It is made of DNA (or
RNA in some viruses) and includes
genes and other elements that
control the activity of those genes.
Genomes of cells are composed
exclusively of DNA, but viruses
contain either DNA or RNA as the
principal genetic material.
It consists of a long
sequence of nucleic acid that
provides the information needed to
construct the organism. The genome
contains the complete set of
hereditary information for any
organism. Although most of the genome exists in the form of chromosomes. Genetic material
can appear in non-chromosomal sites as well. For example, bacteria and some fungi contain tiny
extra pieces of DNA (plasmid) and the mitochondria and chloroplasts of eukaryotes are equipped
with their own functional chromosome.
A chromosome is a discrete cellular structure composed of a neatly packaged DNA
molecule. The chromosome of
eukaryotes and bacterial cells differ
in several respects. The structure of
eukaryotic chromosomes consists
of a DNA molecule tightly wound
around histone protein, whereas a
bacterial chromosome is condensed
and secured into a packet by means
of a different type of protein.
Eukaryotic chromosomes are
located in the nucleus; they vary in
number from a few to hundreds: they can occur in pairs (diploid) or singles (haploid), and they
are linear in format. In contrast, most bacteria have a single circular chromosome, although some
have multiple chromosomes and a few have linear chromosomes. The nucleoid (meaning
nucleus-like) is an irregularly-shaped region within the cell of a prokaryote that contains all or
most of the genetic material. In contrast to the nucleus of a eukaryotic cell, it is not surrounded
by a nuclear membrane.

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All chromosomes contain a series of basic informational ‘packets’ called genes. A gene
can be defined from more than one perspective but in classical genetics, the term refers to the
fundamental unit of heredity responsible for a given trait in an organism. In a molecular and
biochemical sense, it is a portion of the chromosome that provides information for a given
function. Specifically, it is a specific segment of DNA that contains the necessary codes to make
a protein of the RNA molecule.
Genes fall into three basic categories:
i. The structural gene that code for protein
ii. Genes that code for RNA and
iii. Regulatory genes that control gene expression
The sum of all these types of genes constitutes an organism’s distinctive genetic makeup or
genotype. The expression of the genotype creates traits (certain structures or functions) referred
to as the phenotype. For example, a person inherits a combination of genes (genotype) that gives
a certain eye color or height (phenotype), a bacterium inherits genes that direct the formation of a
flagellum or the ability to metabolize a certain substrate, and a virus has genes that dictate its
capsid structure.
Size Range of Prokaryotic Genomes
Genomes of species of both Bacteria and Archaea show a strong correlation between
genome size and open reading frame (ORF) content. Recall that an open reading frame is a
sequence of DNA or RNA that can be translated to yield a polypeptide. Regardless of the
organism, each megabase pair of DNA in a prokaryote encodes about 1000 ORFs. As the size of
prokaryotic genomes increases, the gene number also increases proportionally. This contrasts
markedly with the genomes of eukaryotes, in which noncoding DNA may be a large fraction of
the genome, especially in organisms with large genomes.
Analyzing genomic sequences can shed light on fundamental biological questions. For
example, how many genes are necessary for a cell to exist? The record for the smallest genome
for a free-living organism belongs to a species of Bacteria referred to as strain HTCC2181,
whose genome contains 1,304,428 bp and 1354 genes. This undercuts the previous record holder,
Pelagibacter ubique (1,308,759 bp), a marine heterotroph, by a mere 4331 bp, suggesting that
this is close to the practical limit for independent life. HTCC2181 is an as yet uncultured
methylotrophic bacterium (methylotrophs are organisms that catabolize one-carbon compounds,
such as methanol) that is common in marine coastal ecosystems.
Several other free-living Bacteria and Archaea are known that have genomes of around
1400 genes. These organisms are extremely efficient in their use of DNA. They have few or no
introns, inteins, or transposons and have very short intergenic spaces. The largest prokaryotic
genomes contain over 10,000 genes and are primarily from soil bacteria, such as the
myxobacteria, who undergo complex life cycles.
Perhaps surprisingly, genomic analyses have shown that autotrophic organisms need only
a few more genes than heterotrophs. For example, the methanogen Methanocaldococcus
jannaschii (Archaea) is an autotroph whose genome contains only 1738 ORFs. This enables it to

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be not only free-living, but also to rely on CO2 as its sole carbon source. Aquifex aeolicus
(Bacteria) is also an autotroph and contains the smallest known genome of any autotroph at just
1.5 megabase pairs. Both Methanocaldococcus and Aquifex are also hyperthermophiles, growing
optimally at temperatures above 80°C. Thus, large genomes are not necessary to support
autotrophic and extreme lifestyles.
Small Genomes
The smallest cellular genomes belong to prokaryotes that are parasitic or endosymbiotic
(cells that live inside other cells). Genome sizes for obligately parasitic prokaryotes range from
490 kbp for Nanoarchaeum equitans (Archaea) to 4400 kbp for Mycobacterium tuberculosis
(Bacteria). The genomes of several prokaryotes, including N. equitans, Mycoplasma, Chlamydia,
and Rickettsia, are smaller than the largest known viral genome, that of Mimivirus with 1.2 Mbp.
The degenerate cicada endosymbiont Hodgkinia has a tiny genome, less than 150 kbp.
Genomes smaller than 1.2 Mbp are all found in bacteria that are dependent on other cells
for some aspect(s) of their existence. Mycoplasmas, with genomes of just over 500 kbp and just
under 500 genes, have the smallest genomes among parasitic bacteria. Excluding endosymbionts,
the smallest prokaryotic genome is that of N. equitans, which is some 90 kbp smaller than that of
Mycoplasma genitalium (577 to 590 kbp). Despite this, the genome of N. equitans actually
contains more genes than M. genitalium. This is because the N. equitans genome is extremely
compact with almost no noncoding DNA. N. equitans is a hyperthermophile and a parasite of
another hyperthermophile, the archaeon Ignicoccus. N. equitans lacks virtually all genes that
encode metabolic proteins and presumably depends on its host for most catabolic as well as
anabolic functions.
Using Mycoplasma, which has around 500 genes, as a starting point, it has been
estimated that around 250–300 genes are the minimum number possible for a viable cell. These
estimates rely partly on comparisons with other small genomes. In addition, systematic
mutagenesis has been performed to identify essential genes. For example, experiments with
Escherichia coli and Bacillus subtilis, both of which have about 4000 genes, indicated that
approximately 300–400 genes are essential depending on the growth conditions. However, in
these experiments the bacteria were provided with many nutrients, allowing them to survive
without many genes that encode biosynthetic functions. Most of the “essential genes” identified
are present in other bacteria as well and approximately 70% have also been found in Archaea
and eukaryotes.
Large Genomes
Some prokaryotes have very large genomes that are as large as those of certain eukaryotic
microorganisms. Because eukaryotes tend to have significant amounts of noncoding DNA and
prokaryotes do not, some prokaryotic genomes actually have more genes than microbial
eukaryotes, despite having less DNA. For example, the genome of Bradyrhizobium japonicum, a
bacterium that forms nitrogen-fixing root nodules on leguminous plants such as soybeans, has
9.1 Mbp of DNA and 8300 ORFs, whereas the genome of the baker’s yeast Saccharomyces
cerevisiae, a eukaryote, has 12.1 Mbp of DNA and only 5800 ORFs. The soil bacterium

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Myxococcus xanthus also has 9.1 Mbp of DNA, whereas many of its close relatives have
genomes approximately half this size. It has been hypothesized that multiple duplications of
substantial segments of genomic DNA might account for such very large genomes.
The largest prokaryotic genome known at present is that of Sorangium cellulosum, a
species of the myxobacteria. With just over 13 Mbp on a single circular chromosome, its genome
is roughly three times larger than that of Escherichia coli. The Sorangium genome has a
relatively large proportion of noncoding DNA for a bacterium (14.5%) and consequently has
fewer coding sequences than might have been expected (only 9400). Nonetheless, it has more
DNA than several eukaryotes including yeast and the protozoans Cryptosporidium and Giardia.
In contrast to Bacteria, the largest genomes found in Archaea thus far are around 5 Mbp.
Overall, prokaryotic genomes range in size from those of large viruses to those of eukaryotic
microorganisms.
Eukaryotic Microbial Genomes
The genomes of many microbial eukaryotes have been sequenced, and their size varies
widely. Certain single-celled protozoans, including the free-living ciliate Paramecium (40,000
genes) and the pathogen Trichomonas (60,000 genes), have significantly more genes than do
humans (20,000 to 25,000 genes). Indeed, Trichomonas presently holds the record for largest
gene number of any organism. This is puzzling because Trichomonas is a human parasite, and
such organisms typically have small genomes relative to comparable free-living organisms
because parasites rely on their host for some or even many functions.
Genomes of Microbial Parasites
Apart from Trichomonas, parasitic eukaryotic microorganisms typically have genomes of
10–30 Mbp containing between 4000 and 11,000 genes. For example, Trypanosoma brucei, the
agent of African sleeping sickness, has 11 chromosomes, 35 Mbp of DNA, and almost 11,000
genes. The most important eukaryotic parasite is Plasmodium, which causes malaria. The four
species of Plasmodium that infect humans have genomes ranging from 23 to 27 Mbp, comprising
14 chromosomes with around 5500 genes. About half of these genes have introns and about a
third encode conserved hypothetical proteins of unknown function. The free-living social
amoeba Dictyostelium has about 12,500 genes (but note that Dictyostelium has both single-celled
and multicellular phases in its life cycle), and the pathogenic amoeba, Entamoeba histolytica, the
causative agent of amebic dysentery, has approximately 10,000 genes.
The smallest eukaryotic cellular genome known belongs to Encephalitozoon cuniculi, an
intracellular pathogen of humans and other animals that causes lung infections. E. cuniculi lacks
mitochondria, and although its haploid genome contains 11 chromosomes, the genome size is
only 2.9 Mbp with approximately 2000 genes; this is smaller than many prokaryotic genomes.
As for prokaryotes, the smallest eukaryotic genome belongs to an endosymbiont. Known as a
nucleomorph, this is the degenerate remains of a eukaryotic endosymbiont found in certain green
algae that have acquired photosynthesis by secondary endosymbiosis. Nucleomorph genomes
range from about 0.45 to 0.85 Mbp.

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The Yeast Genome

Of single-celled eukaryotes, the yeast Saccharomyces cerevisiae is most widely used as a
model organism and is also extensively used in both baking and brewing. The haploid yeast
genome contains 16 chromosomes ranging in size from 220 kbp to 2352 kbp. The total yeast
nuclear genome (excluding the mitochondria and some plasmid and virus-like genetic elements)
is 13,400 kbp. Yeast chromosome XII contains a stretch of approximately 1260 kbp containing
100–200 repeats of yeast rRNA genes. In addition to multiple copies of the rRNA genes, the
yeast nuclear genome has approximately 300 genes for tRNAs (only a few are identical) and
nearly 100 genes for other types of noncoding RNA. Yeast has approximately 6000 ORFs, which
is fewer than that of some genomes of Bacteria. About two-thirds of the yeast ORFs encode
proteins whose functions are known.
How many yeast genes are actually essential? This question can be tackled by
systematically inactivating each gene in turn with knockout mutations (mutations that completely
inactivate genes). Knockout mutations cannot normally be obtained in essential genes in a
haploid organism. However, yeast can be grown in both diploid and haploid states. By
generating knockout mutations in diploid cells and then investigating whether they can also exist
in haploid cells, it is possible to determine whether a particular gene is essential for cell viability.
Using knockout mutations, it has been shown that around 900 yeast ORFs (17%) are essential.
Note that this number of essential genes is much greater than the approximately 300 genes
estimated to be the minimal number required in prokaryotes. Because eukaryotes are more
complex than prokaryotes, a larger minimal gene complement would be expected.
Being a eukaryote, the yeast genome contains introns. However, the total number of
introns in the protein encoding genes of yeast is a mere 225. Most yeast genes with introns have
only a single small intron near the 5′ end of the gene. This situation differs greatly from that seen
in more complex eukaryotes. For example, in the worm Caenorhabditis elegans, the average
gene has five introns, and in the fruit fly Drosophila, the average gene has four. Introns are also
common in the genes of plants, averaging around four per gene. The model higher plant
Arabidopsis averages five introns per gene, and over 75% of Arabidopsis genes have introns. In
humans almost all protein encoding genes have introns, and it is common for a single gene to
have 10 or more. Moreover, human introns are typically much longer than human exons, the
DNA that actually encodes proteins. Indeed, exons make up only about 1% of the human
genome, whereas introns account for 24%.
Viral Genomes
All cells contain double-stranded DNA genomes. By contrast, viral genomes consist of
either DNA or RNA and are further subdivided based on whether the genome is single-stranded
or double- stranded. A very few highly unusual viruses use both DNA and RNA as genetic
material, but at different stages of their life cycle.
Viral genomes can be either linear or circular, and single-stranded viral genomes may be
of either the plus sense or minus sense in terms of their base sequence. Viral genomes of the plus
configuration have the exact same base sequence as that of the viral mRNA that will be

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translated to form viral proteins. By contrast, viral genomes of the minus configuration are
complementary in base sequence to viral mRNA. Viral genomes are typically smaller than those
of cells. The smallest bacterial genome known is about 145 kilobase pairs, encoding about 170
genes. Most viral genomes encode from a few up to about 350 genes. The smallest viral genomes
are those of some small RNA viruses that infect animals. The genomes of these tiny viruses
contain fewer than 2000 nucleotides and only two genes. A few very large viral genomes are
known, such as the 1.25-Mbp DNA genome of a marine virus called Megavirus, which infects
protozoans. RNA viruses typically have the smallest genomes and only DNA viruses have
genomes encoding more than 40 genes. Viruses can be classified on the basis of the hosts they
infect as well as by their genome structure. Thus, we have bacterial viruses, archaeal viruses,
animal viruses, plant viruses, protozoan viruses, and so on. Bacterial viruses are called
bacteriophages (or simply phage for short) and have been intensively studied as model systems
for the molecular biology and genetics of virus replication.

The Size of DNA Molecule -Units of Length

DNA molecules are huge in size. On an average, a pair of B-DNA with a thickness of
0.34 nm has a molecular weight of 660 daltons. For the measurement of lengths, DNA double
stranded structure is considered, and expressed in the form of base pairs (bp). A kilobase pair
(kb) is 103 bp, and a mega base pair (Mb) is 106 bp and a giga base pair (Gb) is 109 bp.
It may be noted here that the lengths of RNA molecules (like DNA molecules) cannot be
expressed in bp, since most of the RNAs are single-stranded.
The length of DNA varies from species to species and is usually expressed in terms of
base pair composition and contour length. Contour length represents the total length of the
genomic DNA in a cell. As we know that the distance between two bases is 0.34 nm.
 In λ phage virus, total base pair present is 4.8 x 104 bp so its contour length is 16.5 µm
 In E. coli, total base pair present is 4.6 x 106 bp so its contour length is 1.5 mm.
 In Diploid human cell (46 chromosomes), total base pair present is 6.0 x 10 9 bp so its
contour length is 2 meters.

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