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In short…
• Genome anatomy
– Eukaryotes
– Prokaryotes

• Genome evolution

• Genome sequencing

• Genome viewers
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Difference – Genetics and Genomics

• Genetics scrutinizes the functioning and

composition of a single gene

• Genomics addresses all genes and their inter

relationships in order to identify their combined
influence on the growth and development of the
organism

(WHO)

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 Introduction
• Genome – the entire genetic complement of a
living organism (Brown, TA. Genomes, 1999)

Chloroplast

Mitochondria

Nucleus

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 Genome anatomy
• Different genome anatomies:

Eukaryotes
Root

Prokaryotes
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 Genome anatomy
Species Genome size (Mb) Number of genes
Eukaryotes
Homo sapiens 3,200 30,000
Arabidopsis thaliana 125 25,500
Saccharomyces cerevisiae 12 5,800
Bacteria
Escherichia coli 4.6 4,400
Mycoplasma genitalium 0.6 500
Archaea
Methanococcus jannaschii 1.7 1,750
Archaeoglobus flugidus 2.2 2,500
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 Genes

• Basic unit of heredity

(traits are passed from
parents to their children)
• Different nucleotides
spell out codes, or
genes
• Genes tell the cell which
specific proteins it
should make
 Genome
• A genome is the entire genetic make-up of an
organism
• The human genome refers to all the DNA found in
humans
• Each type of plant and animal has its own genome
• The human genome is like a map of an immense
country that has three billion unmarked streets
• A map of the human genome can be used to show
where genes are in relation to one another along the
chromosome
 Gene Expression

• When making a protein, the cell copies

the gene
• Sends the copy from its nucleus to its
ribosomes
• This copy is called messenger RNA, or
mRNA
• mRNA contains only the coding part of
the gene
 Genomics

• The study of the entire genetic complement of

any organism
• It encompasses many fields and involves many
wet lab and dry lab techniques
• The basis of the field of bioinformatics
Components of Genomics
Components of Genomics
 Genome anatomy
• Is the organism‟s complexity correlated with
the number of chromosomes (K value)?

Homo sapiens Lysandra atlantica

46 250 13
 Genome anatomy
• Is the organism‟s complexity correlated with
the number of genes (N value)?

Drosophila melanogaster Caenorhabditis elegans

~13,700 ~20,500 14
 Genome anatomy
• Is the organism‟s complexity correlated with
length of the genome (C value)?

Homo sapiens Amoeba dubia

~3,000,000,000 670,000,000,000
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 Genome anatomy
• The genome size (C value) varies
significantly from species to species.

• Solution
The genome size is determined by the
„packing of the genes‟ (introns, genome
wide repeats, junk DNA, etc).

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 Genome anatomy
• Physical organization

• Distribution of genes

• “Extras”

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 Genome evolution
• How did genomes evolve from the “cell-stage”?

• Generally genomes have become bigger, more

“complex”, and richer in genes:
– Duplication events

– New genes from other species (HGT)

– Noncoding DNA evolution

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 Prokaryotes - Physical organization
• A single circular DNA
molecule

• Super coiled loops

• Centered around a
protein core

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Prokaryotes - Physical organization
• Many known exceptions from the “one circular
genome” model are known today

• Mega plasmids (Vibro cholerae)

• Linear DNA molecules (Borrelia burgdorferi)

• Multiple molecules (Deinococcus radiodurans)

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 Prokaryotes – gene distribution
Species Genome size (Mb) Number of genes
Eukaryotes
Homo sapiens 3,200 30,000
Arabidopsis thaliana 125 25,500
Saccharomyces cerevisiae 12 5,800
Bacteria
Escherichia Coli 4.6 4,400
Mycoplasma genitalium 0.6 500
Archaea
Methanococcus jannaschii 1.7 1,750
Archaeoglobus flugidus 2.2 2,500
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 Prokaryotes – gene distribution
• The genome of prokaryotes is compact and
efficient
• Typically ~90% of the genome codes for
protein or structural RNA (the genome length
is correlated to the number of genes)

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 Prokaryotes – “extras”
• Plasmid - A DNA segment (usually circular) that
coexists with the main chromosome

• The plasmid carries “extra” genes that are not

encoded in the chromosome

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Eukaryotes - Physical organization
• A set of linear DNA molecules, tightly packed
with histones

• The genome is divided to chromosomes (at

least one or more)

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 Eukaryotes – gene distribution
• Genes are not distributed evenly along
the chromosome

• Some regions are almost without

genes, e.g., centromere

• In plant genomes genes, are clustered

together, divided by gene-deserts

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 Eukaryotes – “extras”
• Eukaryotic cells usually contain organelles which
have genomes of their own (mitochondrion,
chloroplast, etc.)

• The organelle genome is usually circular and

found in multiple copies within a single organelle

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 Eukaryotes – “extras”
Origin of organelles – The endosymbiont theory
• Observation - Organelle genes are more closely
related to bacterial genes
- expression process similar to bacteria

• Theory – organelles are relics of free living bacteria

that had a symbiosis with the ancestral eukaryotic cell

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 Eukaryotes – “extras”
• The organelle codes for rRNA, enzymes for the
respiratory chain, tRNAs, ribosomal proteins,
transcription and translation enzymes, transport
enzymes

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 DNA Sequencing
• Two basic approaches that were developed in
the mid-1970s:

– Chain termination method (Sanger-Coulson method)

– Using a single strand of DNA to partly synthesize a
complementary strand

– Chemical degradation method (Maxam-Gilbert

method) – Treatment of DNA with chemicals in order
to cut the molecule at specific locations

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 DNA Sequencing

Requires 4 parallel
experiments, for
each type of ddN

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 DNA Sequencing

Automated sequencing
with different fluorescent
label for each type of ddN

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 Genome sequencing
• Sequencing of a whole genome poses a new
problem (automate sequencing is limited to
~1500 nucleotide length):

How can we sequence longer fragments?

1. Shotgun approach
2. Clone contig approach

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 Genome sequencing
Last comments:
• “Finished” sequences are sequenced 8-10 times
(before that they are considered “draft”)

• Some parts of the genome are extremely difficult to

sequence:
1. Repetitive region, e.g., centromere
2. Constitutive heterochromatin (tightly packed DNA regions)
3. They are sometimes absent from the final version

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 Genome viewers
• A Genome viewer is a program that enables
the user to move along the genome & obtain
various types of data
• The viewer incorporates information from
various databases

– For sequenced genomes

– Model organisms usually have specialized
genome viewers

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 Genome viewers
• A perfect viewer?
1. User friendly – locating, moving, zooming.
2. Genes – annotated, predicted, ORF.
3. RNA – known mRNA, EST.
4. Mutations – SNP.
5. Mapping – STS, Giemsa band.
6. Conserved regions, genome repeats.
7. Links.
8. Download options!!!.

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 Genome viewers
• NCBI offers relatively simple genome viewers.

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 Genome viewers - UCSC
• UCSC genome viewer – Human, rat, mouse,,
fruit fly, C. elegans, etc.

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 Genome viewers - UCSC
• Example: Human hemoglobin beta

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Any Queries???

Thank You!

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