Genomic sequencing a sub-disciplinary branch of genetics and difference between the two sequencers used to sequence the genome basically automated sequencer and fluorescence sequencers and its applications.

1. GENOME SEQUENCING
BY :-
ANITHA.Y
14KUST4002

2. WHAT IS GENOMICS ?

3. GENOMICS AS A SUB DISCPLINARY
BRANCH
• MAPPING
• FUNCTIONAL
ANALYSIS OF GENOME
• SEQUENCING

4. DIFFERENCE B/W GENETICS
AND GENOMICS
looks at a single
gene where as
examines
all the genes of entire
system in a broader
manner.
• It deals with the Study of
functional and structural
aspects of genome aiding
in
.

5. TYPES OF
GENOMICS
STRUCTURAL
FUNCTIONAL
COMPARATIVE
STRUCTURAL-
Determination of complete
sequence and gene map.
FUNCTIONAL-
Functioning and
regulation of gene
expression ; metabolic
pathway etc
COMPARATIVE-
Compares genes from
different genomes to
relate functional and
“evolutionary
relationships”.

6. GENOME
 IS DEFINEDAS
.
OR
INA E/K , DNA OR RNA OR
VIRUSES.
 IT IS DENOTEDAS ‘X’.NUMBEROF PLOIDYOF AN ORGANISM.
 EXAMPLE :- DROSOPHILA MELANOGASTER (2n=2X=8)GENOME
:- X=4
 TRITICUMAESTIVUM (6n=6X=42)GENOME :- X=7
 THETERM WAS
TO DENOTE COMPLETE SET OF CHROMOSOMALAND
EXTRACHROMOSOMALGENES IN ALL ORGANISM INCLUDING
VIRUS.

7. TYPES OF GENOME
PROKARYOTIC GENOME
EUKARYOTIC GENOME
• NUCLEAR GENOME
• MITOCHONDRIAL GENOME
• CHLOROPLAST GENOME

8.  Is a technique that allows researchers to read
the genetic information found in the DNA of
anything from bacteria to plant to animals.
 It basically involves “determination of order
of bases ”.
AGCTTAACCCTGGTACCAAAGGGTCACTT
 Position of every gene along the
chromosome, regulatory gene that flank each
gene, the coding sequence that determines
the protein produce by each gene.

9. WHY SEQUENCE GENOME ? ? ?
IMPROVE
HUMAN HEALTH
HARNESS
NATURAL
ENERGY
CONSERVE
ENVIRONMENT
ENSURE FOOD
SAFETY
CLEAN UP
ENVIRONMENT

10. WHY SEQUENCE GENOME ? ? ?
 DISTINGUISH B/W GENOMES OF FLORA AND FAUNA ,
ANDTHEN GROUPTHEMTOWHICH FIELDTHEY
BELONG.
 SERVES AS A MEANS OF CROP IMPROVEMENT AND
DEVELOP CONVENTIONAL BREEDING PRACTICESTO
DEVELOP AGRICULTURAL PRACTICES.
 IT CAN ALSO BE USEDTO PRODUCE SUFFICIENT
AMOUNT OF SAFE AND NUTRITIOUS FOOD DURING
INCREASE POPULATION DEMAND.
 HELP RESEARCHES OR PRODUCERS (FARMERS) IN
DETERMINING THE RELATIONSHIP B/W STRESS AND
THEYIELD POTENTIALTHUS HELPING IN IMPROVING
VARIETIES.

11. MILESTONES
 1977- FIRST SEQUENCEDΦx 174 BACTERIOPHAGE GENOME
(F.SANGER) (5,375bp)
 1995- HAEMOPHILUS INFLUENZAE (1,830,137bp) ; MYCOPLASMA
GENITALIUM (5,80,000bp)CRAIGVENTER AND HAMILTON SMITH)
 1996- SACCAROMYCES CEREVISIAE (12,068,000)
 1997- ESCHERICHIA COLI (4,639,221bp)
 2000- DROSOPHILA MELANOGASTER (180,000,000bp)
 2001- HUMANWORKING DRAFT (320,000,000bp)
 2002-PLASMODIUM FALCIPARUM (23,000,000bp) ;ANOPHELES
GAMBIEA (278,000,000bp)
 2003- HUMAN FINISHED SEQUENCE (3,200,000,000bp)
 2005- ORYZA SATIVA (489,000,000bp)
 2006- POPULUSTRICHOCARPA (485,000,000bp)

12. SEQUENCING OF OTHER ORGANISM
 The sequence of many organisms have been carried
out at a rapid pace
 There are many medical ; genetics ; and commercial
reasons for sequencing genomes of other organisms
:-
 Escherichia coli
 Saccharomyces cerevisiae
 Caenorhabditis elegans
 Drosophila melanogaster
 Arabidopsis thaliana(Thale / Mouse ear cress)
 Oryza sativa L. (Rice)
 Mus musculus(laboratory mouse)

13. DETERMINING THE SEQUENCE OF DNA
 METHODS :-
 MAXAM & GILBERT CHEMICAL DEGRADATION METHOD
 FREDRICK SANGERS CHAINTERMINATION METHOD
 GENOME SEQUENCING METHODS :-
 - SHOT GUN SEQUENCING
 - CLONE CONTIG APPROACH
 - AUTOMATED SEQUENCER
 - FLUORESCENCE SEQUENCER
 2nd GENERATION SEQUENCING METHOD :-
 - PYRO SEQUENCING
 - NANOPORE SEQUENCING
 - ILLUMINA SEQUENCING
 - SOLID SEQUENCING
 3rd GENERATION SEQUENCING METHOD

14. AUTOMATED SEQUENCER
• First automated sequence was
invented by Llyod. M.Smith.
• It uses the Sangers sequence
method and formed the basis of
first generation of Dna sequences.
• The 1st automated sequencer was
AB370A which was able to
sequence 96 samples
simultaneously with 500-600kb in
size.
• Later in 1955 AB310 took over and
completed the ‘’ human genome
project “ in 2001
• The manufactures of this sequencer
are Roche , Illumina ,Life
Technologies ,Beckman
coulter,Pacific biosciences and
Oxford nanopore.

15. AUTOMATED SEQUENCER
• It is basically radio active
sequencing approach.
• The electrophoretic bands gets
activated by scanning laser.
• The colour is read by and then
the computer assembles the
images as electropherograms
• They analyse the resulting
electropherograms giving the
output as four colour
chromatogram.
• There are many software tools
which are optimized for
sequencing the data like
preassemble ,seqtrace etc.

16. FLUORESCENCE
SEQUENCER• Since it was radio active in
nature there were disposable
problems and health risks
• Hence fluorescence sequencer
used fluorescent dyes .
• Sequencing products are
electrophoresed and they use
laser to detect fragments.
• Incorporation of randomly
labelled ddNTPs produces a
series of fragment in which
chain growth has been
terminated at each successive
position.
• Each nucleotide will be longer
than the previous one.
• Separation of fragments for
determining the order by size in
the form of ladder and as a
series of coloured band.
• Polyphred is a software tool.

17. As of september 2007, complete
sequence was known :
1879 viruses
577 bacterial species
Approx 23 E/K species (mostly half are viruses)

19. REFERENCES:-
 Brown B,Aoran M (2001)The rise of modern
genomics,3rd ednWiley,NewYork,p234-295
 C.A Graham and A.J.M Hill, vol 167: Dna sequencing
protocols,p645-660
 Bishop, J.E &Waldholz M.Genome (Simon and
Schuster New york,1990),p109-117
 Aoran MThe future of genomics ,proceedings of the
genomics researchers,boston (e-book)
 Springer
 Research gate