basic of the genome content,types of genomes,its size, factors altering the genome size, Genome complexity and c-value paradox

1. Content of the Genome
FBT-601 Advances In
Molecular And Cell
Biology

2. • Genome – “The complete set of genetic information in an organism”. It consist of nucleotide sequences of
DNA (or RNA/RNA viruses). The term was created in 1920 by Hans Winkler-Germany.
• The study of the genome is called Genomics.
• It includes both genes (coding) and non-coding DNA, mitochondrial DNA & chloroplast DNA.
• The genome is a store of biological information, but on its own it is unable to release that information to
the cell. Utilization of the biological information contained in the genome requires the coordinated activity
of enzymes and other proteins, which participate in a complex series of biochemical reactions referred to
as Genome expression.

3. • Within the genome, much of the critical information is found in discrete regions referred to as Genes.
A gene is typically defined as a region of DNA that controls a discrete, hereditary characteristic, and
as such usually specifies the production of a functional product (a protein or RNA molecule).
• Three types of Genome
1. Prokaryotic genomes: DNA genomes- Archaea and most bacteria have a single circular chromosome.
While, some bacterial species have linear or multiple chromosomes. Most prokaryotes have very
little repetitive DNA in their genomes.
2. Eukaryotic genomes: Eukaryotic genomes are composed of one or more linear DNA chromosomes.
Eukaryotic Genomes Contain Non-repetitive and Repetitive DNA Sequences.
• Two general types of genomic sequences –
• A. Non-repetitive DNA : There is only one copy in a haploid genome.
• B. Repetitive DNA consists of sequences that are present in more than one copy in each haploid
genome.
3. Viral genomes: 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.

4. Genome size
• Genome size - The amount of DNA contained in a haploid genome expressed either in terms of the
number of base pairs, kilobases (1 kb = 1000 bp), or mega-bases (1 mb = 1 000 000 bp), or as the mass of
DNA in picograms (1 pg = 10−12 g).
• Its varies widely across species.
• Invertebrates have small genome. Its correlated to a small number of transposable.
• 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 (evolution). Before this loss, DNA methylation allows the adequate expansion of the genome.
• In prokaryotes (Archaea and Bacteria) there is, in general, a linear relationship between genome size and
the number of genes. The smallest genomes are found in symbionts and parasites, as they undergo a gene
degradation process during adaptation to their new lifestyle.
• Genome sizes among vertebrates range from 0.5 to 150 pg, among the insects from 0.05 to 15 pg, and
among the annelid worms from 0.7 to 8 pg. Within one genus of salamanders, Plethodon, genome sizes
for different species range from 18 to 69 pg.
• There is no clear and consistent correlation between morphological complexity and genome size in either
prokaryotes or lower eukaryotes.
• The main reason why there is such a big variety of sizes is due to the presence of transposable elements.
TEs are known to contribute to a significant change in a cell's mass of DNA.

5. MOLECULAR MECHANISMS THAT ALTER GENOME SIZE
Range of genome size in organisms of the three
domains of life.
• There are many mutational mechanisms that can
produce changes in genome size.
• The probability of one or the other occurring depends
on evolutionary mechanisms such as natural selection
(whether it provides an advantage or disadvantage to
the individual) or genetic drift (random).
• Chromosomal mechanisms often produce drastic
changes with a single mutation.
• The mobile genetic elements or transposable
elements, are other causes of large variations in
genome size (nucleotides, duplicate copies of genome
parts).
• Spontaneous insertions or deletions (called indels) of
a few nucleotides are one of the most important
causes of the development of the size of the genome.
• The variation in the length of the DNA of the
minisatellites and microsatellites is another
mechanism which can alter the size of the genome.

6. Organism type Organism name Genome size (BP) Remarks
Viruses Bacteriophage MS2 3.5 kb First sequenced RNA-genome
Phage Φ-X174 5.4 kb First sequenced DNA-genome
Phage λ 48.5 kb Often used as a vector for the cloning of
recombinant DNA.
Bacterium Haemophilus influenzae 1.8 MB First genome of a living organism
sequenced, July 1995
Nostoc punctiforme 9 MB 7432 open reading frames
Fungus – yeast Saccharomyces cerevisiae 12.1 MB First eukaryotic genome sequenced, 1996
Nematode Caenorhabditis elegans 100 MB First multicellular animal genome
sequenced, December 1998
Mammal
Homo sapiens 3 GB
Homo sapiens genome size estimated at 3.2
Gbp in 2001
Fish
Tetraodon nigroviridis 390 MB
Smallest vertebrate genome known
estimated to be 340 Mb
Protopterus aethiopicus 130 GB Largest vertebrate genome known

7. Genome Complexity
• The relative amounts of repeated and unique (or single copy) DNA
sequences in an organism’s genome as its genomic complexity.
• Prokaryotic genomes have a lower genomic complexity than
eukaryotes.
• Using the same data as is in the previous two graphs, Britten and
Davidson demonstrated the difference between eukaryotic and
prokaryotic genome complexity by a simple expedient.
• Instead of plotting the fraction of dsDNA formed vs. time of
renaturation, they plotted the percent of re-associated DNA against
the concentration of the renatured DNA multiplied by the time that
DNA took to reanneal (the CoT value).
• When CoT values from rat and E. coli renaturation data are plotted
on the same graph, you get the CoT curves in the graph below.
• CoT curves tell us that ~100% of the bacterial genome consists of
unique sequences, compared to the rat genome with its three DNA
redundancy classes.
• Prokaryotic genomes are indeed largely composed of unique (non-
repetitive) sequence DNA that must include single-copy genes (or
operons) that encode proteins, ribosomal RNAs and transfer RNAs.

8. C-value Paradox
• C-value for a species is defined as the amount of DNA in picograms (g x10-12) in one haploid set
of chromosomes from a non-dividing, somatic cell of an organism belonging to that species.
• The mismatch between the C-values and the presumed amount of genetic information contained
within the genomes was called C-value paradox.
• The C-value paradox can be resolved on the following three grounds:
1. Genome size differences among eukaryotes are mainly the result of different amounts of
noncoding repetitive DNA sequences and different levels of repetition of coding and noncoding
sequences.
2. There is no C-value paradox at the levels of metabolism and development, as determined by
complexity of messenger RNA, that is, the transcriptive capacity of the genome.
3. the differences in genome size (the nucleotype) between related organisms and the wide
differences in chromosome number and shape (karyotype) that are also found within families and
genera, it is essential to uncouple the coding informational component of the genome from
nucleotype and karyotype.