1. Genome Analysis Assaad text book slides only Lectures by F. Assaad can be downlaoded from http://www.botanik.biologie.tu- muenchen.de/~farhah/index.htm

2. Genetic Maps Genetic maps were initially based on visible markers First detailed genetic map of Arabidopsis published in 1983 Most mutations are “silent”. More abundant molecular markers were used for high resolution genetic maps.

3. Genomic Libraries for Physical Maps Long chromosomal fragments (~ up to 350 kb) can be cloned into BAC vectors oriS and repE mediate the unidirectional replication of the F factor

4. Fingerprint (restriction digest separated on gel) of BAC clones

5. DNA fingerprints can be used to align BAC clones. In addition, 18,300 BAC end sequence reads were used to generate a physical map.

6. Sequencing of ordered clones

7. Science 2002. 296: 61.

8. Scrambled blocks of genes in common between the human and the mouse.

9. Text Book Readings Modern Genetic Analysis Integrating genes and genomes 2 nd edition. Giffiths and Lewontin Chapter 4Mitosis vs Meiosis Chapter 6 Recombination, Linkage Chapter 9 Genomics For next lecture see pages 303-305. Genes VIII, Benjamin Lewin ISBN 013144946X

10. References Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. THE ARABIDOPSIS GENOME INITIATIVE Nature 408: 796-815. 2000. The Draft Sequence of the Rice Genome. 2002. Science 296: 92-100. (Syngenta)

11. Vocabulary PCR, meiosis, recombination, segregation (should know) cDNA EST (Expressed Sequence Tag) Genetic and Physical maps Linkage (Kopplung) BAC (Bacterial Artificial Chromosome) SSLP (Simple Sequence Length Polymorphism) Shotgun vs ordered clone sequencing Minimal tiling path Contig (contiguous sequences) Protein family and protein domain

12. October 24thAssaadGenome Analysis November 14thGierlTranscriptome, Proteome, Metabolome November 21stGrillGene Identification November 28thAssaadForward versus Reverse Genetics December 5thAssaadVesicle Traffic, Cell Wall December 12thAssaadFunctional Interactions December 19thGrillGene Structure January 9thGrillGene Expression, Regulation 1 January 16thGrillProtein Modifications, Regulation 2 January 23rdGrillSignaling January 30thAssaadWhat we have learnt