GENOME ANATOMIES

• In general, prokaryotic genomes are smaller

than eukaryotic genomes.
• Eukaryotic genome sizes vary widely and
are not linked to organismal complexity.
 SIZE OF GENOME APPROX NUMBER REFERENCES
Mb OF GENES
EUKARYOTES

Arabidopsis 125 25,500 AGI, 2000

thaliana
Caenorhabditis 97 19,000 CESC,1998
elegans
Drosophila 180 13,600 Adams et al, 2000
melanogaster
Homo sapiens 3200 30,000-40,000 Venter et al, 2001

Saccharomyces 12.1 5800 Goffeau et al, 1996

cerevisiae
BACTERIA

E.coli 4.64 4400 Blattner et al, 1997

Mycoplasma 0.58 500 Fraser et al, 1995

genitalium
 Compactness of Genomes
FEATURE YEAST FRUIT FLY HUMAN

GENE DENSITY 479 76 11

Average number
per Mb

INTRONS PER GENE 0.04 3 9

AMOUNT OF THE 3.4% 12% 44%

GENOME TAKEN
UP BY GENOME
WIDE REPEATS
• Features of prokaryotic genomes
• The genomes of eubacteria and archaebacterial
cell are more compact; essentially all of their
DNA is functional, that is , contain genes or
gene regulatory elements.
• The sizes of prokaryotic genomes range from
about 1 million to 10 million base pairs of DNA,
usually in a single, circular chromosome.
• Genes in a biochemical pathway or signaling
pathway are often clustered together and
arranged into operons where they are
transcribed as a single mRNA that is translated
to make all the proteins in the operon.
• The size of prokaryotic genomes is directly
related to their metabolic capabilities- the more
genes, the more proteins and enzymes they
make.
• Some prokaryotes have a unipartite genome
like E.coli, which is a single circular DNA
molecule. In addition, plasmids are present in
prokaryotic cells which are smaller circular
DNA molecules. Genes carried on them code for
antibiotic resistance or degradation of complex
organic compounds ,giving them advantage to
survive better in adverse environmental
conditions.
• Borrelia burgdorferi has a linear chromosome
of 911kb, carrying 853 genes as well as 17 or 18
linear and circular molecules which contribute
533kb and 430 genes. Known as multipartite
genomes.
• The average length of a bacterial gene is about
two thirds that of a eukaryotic gene.
• No introns are present in the genes of
prokaryotes.
• Infrequency of repetitive sequences.
Prokaryotic genomes do not have the high copy
number genome wide repeat families found in
eukaryotes. Insertion sequences may be present
as examples of transposable elements.
• EUKARYOTIC GENOMES
• The genome sizes of eukaryotes are
tremendously variable, even within a
taxonomic group ( so called C value
paradox)
• Eukaryotic genomes are divided into
multiple linear chromosomes; each
chromosome contains a single linear duplex
DNA molecule.
• Eukaryotic genes in a biochemical pathway
are not organized into operons; one mRNA
makes one protein.
• Many eukaryotic genes are split; non coding
introns must be removed and the exons spliced
together to make a mature mRNA. Introns are
intervening sequences in genes that do not code
for proteins.
• The multiple exons in a eukaryotic gene can be
spliced in many different ways to make multiple
mRNAs and multiple proteins from a single
gene ( alternative splicing)
• The majority of human genes can be spliced in
two or more different ways. Therefore, the
actual number of human proteins far exceeds
the number of protein coding genes.
• Alternative splicing often results in “tissue
specific” versions of the same gene, say one
spliced variant is present in cardiac muscle,
while a different spliced variant of the same
gene is present in skeletal muscle.
• There is no good correlation between body
size or complexity of an organism and the
size of its genome. The genome size
variation is due mostly to varying amounts
of non coding DNA.
ORGANISM CHROMOSOME BASE PAIRS NUMBER OF GENES
NUMBER DIPLOID

YEAST 16 12.1Mb 5800

FRUIT FLY 8 180Mb 13,600

C.elegans 6 97Mb 19,000

HUMAN 46 3200Mb 19,000

MOUSE 40 3300Mb 20,000

RICE 24 430Mb 37,000

• C value paradox
• Each species has a characteristic content of DNA, which is constant in all
individuals of that species and has thus been called the C value.
• Eukaryotes vary in DNA content but contain much more DNA than
prokaryotes.
• E.coli has 4,600,000 base pairs and about 4000 genes.
• Nematode C. elegans has 20 times more DNA than E.coli, fruit fly
Drosophila melanogaster has 40 times more.
• Vertebrates have greater DNA content( about 3pg), about 700 times
more than E.coli.
• One of the highest DNA contents is that of the salamander Amphiuma,
which has 84pg of DNA, but not 30 times more genes than humans.
• Man has 3pg of DNA per haploid genome or 3 billion bp(base pairs), and
not more than 20,000 genes.
• This means that, the number of genes has no correlation with the
amount of DNA . As is known, most of the DNA in eukaryotic genomes is
non coding as well as repetitive.
• This says that there is no correlation between the morphological
complexity of eukaryotic organisms and their DNA content.
• Reference : CELL AND MOLECULAR BIOLOGY BY DE ROBERTIS & DE ROBERTIS
C value is the amount in picograms, of DNA
contained within a haploid nucleus ( a gamete) or
one half the amount in a diploid somatic cell of a
eukaryotic organism.
Coined by Henson Swift in 1950.
C values vary a lot among species. In animals they
range more than 3300 fold and in plants they differ
by a factor of about 1000.
Variation in C value bears no relationship to the
complexity of the organism or the number of genes
contained in its genome; for example, some single
celled protists have genomes much larger than
humans.
The C value enigma or C value paradox refers to the
extensive variation in nuclear genome size among
eukaryotic species.

Genome size does not correlate with organismal

complexity; cells of salamanders may contain 40 times
more DNA than humans.

The discovery of non coding DNA in the early 1970s

resolved the main question of the C value paradox:
genome size does not reflect gene number in eukaryotes
since most of their DNA is non coding and therefore
does not consist of genes.
The human genome comprises less than 2% protein coding
regions, with the remainder being various types of non
coding DNA especially transposable elements.

C value enigma was coined by Dr T Ryan Gregory a

Canadian biologist of the University of Guelph in 2001.