Genome sequencing

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 Genetics looks at a single gene where as genomics 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 interaction of genes with the loci and alleles .

5. 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 DEFINED AS “WHOLE HEREDITARY INFORMATION OF AN ORGANISM THAT IS ENCODED IN THE DNA” . OR “ONE SET OF GENETIC INFORMATION FROM A HAPLOID SET OF CHROMOSOMES OF A SINGLE CELL” IN A E/K , DNA OR RNA OR VIRUSES. IT IS DENOTED AS ‘X’.NUMBER OF PLOIDY OF AN ORGANISM. EXAMPLE :- DROSOPHILA MELANOGASTER (2n=2X=8) GENOME :- X=4 TRITICUM AESTIVUM (6n=6X=42) GENOME :- X=7 THE TERM “GENOME” WAS 1 st TERMED BY H. WINKLER IN 1920 TO DENOTE COMPLETE SET OF CHROMOSOMAL AND EXTRACHROMOSOMAL GENES IN ALL ORGANISM INCLUDING VIRUS.

7. TYPES OF 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 ”. A G C TT AA CCC T GG T A CC AAA GGG T C A C TT Position of every gene along the chromosome, regulatory gene that flank each gene, the coding sequence that determines the protein produce by each gene. GENOME SEQUENCING

9. WHY SEQUENCE GENOME ? ? ?

10. WHY SEQUENCE GENOME ? ? ? DISTINGUISH B/W GENOMES OF FLORA AND FAUNA , AND THEN GROUP THEM TO WHICH FIELD THEY BELONG. SERVES AS A MEANS OF CROP IMPROVEMENT AND DEVELOP CONVENTIONAL BREEDING PRACTICES TO DEVELOP AGRICULTURAL PRACTICES. IT CAN ALSO BE USED TO 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 THE YIELD POTENTIAL THUS HELPING IN IMPROVING VARIETIES .

11. MILESTONES 1977- FIRST SEQUENCED Φ x 174 BACTERIOPHAGE GENOME (F.SANGER) (5,375bp) 1995- HAEMOPHILUS INFLUENZAE (1,830,137bp) ; MYCOPLASMA GENITALIUM (5,80,000bp) CRAIG VENTER AND HAMILTON SMITH ) 1996- SACCAROMYCES CEREVISIAE (12,068,000) 1997- ESCHERICHIA COLI (4,639,221bp) 2000- DROSOPHILA MELANOGASTER (180,000,000bp) 2001- HUMAN WORKING 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- POPULUS TRICHOCARPA (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 CHAIN TERMINATION METHOD GENOME SEQUENCING METHODS :- - SHOT GUN SEQUENCING - CLONE CONTIG APPROACH - AUTOMATED SEQUENCER - FLUORESCENCE SEQUENCER 2 nd GENERATION SEQUENCING METHOD :- - PYRO SEQUENCING - NANOPORE SEQUENCING - ILLUMINA SEQUENCING - SOLID SEQUENCING 3 rd 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 1 st 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 :

18. FUTURE PROSPECTS

19. REFERENCES :- THANK YOU ONE AND ALL !! Brown B,Aoran M (2001) The rise of modern genomics,3 rd edn Wiley,New York,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 M The future of genomics ,proceedings of the genomics researchers,boston (e-book) Springer Research gate