1. What Is Genomics? Genomics is the study of how the entire genome of a species functions as a unit and evolves over time. It is the study of life’s blueprint, life’s diversity, and life’s history. Bioinformatics: Analyses the information content of genomes. Comparative Genomics: Compares genome sequences with each other to infer evolutionary relationships and mechanisms of evolution. Functional Genomics: Probes how genomes function, as a whole, to give rise to organisms. Ecological Genomics: Understands how genomes, and the organisms they encode, fill specific environmental niches.

2. >500 complete microbial genomes 730 in progress

3. Why Sequence Whole Genomes? To speed characterization of genes mapped by linkage To obtain a "parts list" for what makes up an organism. To discover what sets of genes make organisms (and each of us) similar to and different from one another. To understand our evolutionary heritage. Our genomes are a reflection of our recent and ancient origins.

5. Dideoxy “chain termination” DNA sequencing- Sanger v1, continued

6. Dideoxy “chain termination” DNA sequencing- Sanger v2 !! Fred Sanger, SECOND Nobel Prize in 1980 (Chemistry; his first was in 1958 for methods for determining amino acid sequences in proteins). Made easily robot friendly. High throughput DNA sequencing has allowed the sequencing of whole Genomes. This has driven the Genomics revolution.

8. Sheared and ssDNA Oil emulsion: 1 template/bead Polony: clonal amplification Polony + enzyme beads Picoliter plate The Next Gen Technologies: Pyrosequencing (454, Roche) First of the ‘parallel’ sequencing platforms.

9. Sequencing-by-synthesis Pyrosequencing 3’ATCGTTGCACGTCGACGTA 5’TAGCAAC G dGTP PP i ATP ATP sulfurylase Luciferase 400K reads X 400 bases = 16-20 Mb in 4 hrs! So, 125 Mb is only 6 runs for 1X coverage!

10. Sequence by synthesis – one base at a time Each base has a different color Each base has a reversible terminator The Next Gen Technologies: Illumina (Solexa)

11. DNA Single molecule array Sample preparation Cluster growth 5’ 3’ G T C A G T C A G T C A C A G T C A T C A C C T A G C G T A G T 123789456 Image acquisition Base calling T G C T A C G A T … Sequencing 5 million clusters / channel; 8 channels / flow cell = 40 million reads times ~35 cycles (bases) = 120 billion bases in 3 days (1.2Gb) The Next Gen Technologies: Illumina (Solexa)

12. Sanger Shotgun 454Solexa CloningYesNo ChemistrySangerpyrosequencingreversible terminators DNA bases per $ Human (1X!!) $ 1000 3,000,000 50,000 60,000 500,000 6,000 TimeA really long time 4 hours4 days AccuracyConsensus 99.99% Worst of the 3; not good with homopolymer repeats 1-3% errors Assembly Computational tools BestOKHorrible Gap Closure and Finishing PainPain in the rearROYAL Pain in the rear Technology Development drives Biology

13. First, we've learned that we have a lot to learn Over 35% of genes in ANY organism (including Human) have no deducible function!