1. BIOL 433 Plant Genetics Term 2, 2012-2013 Instructors: Dr. George Haughn Dr. Ljerka Kunst BioSciences 2239BioSciences 2237 822-9089 Tel. 822-2351 george.haughn@ubc.cageorge.haughn@ubc.caljerka.kunst@ubc.cakunst@ubc.ca Dr. Xin Li MSB 317 822-3155 xinli@msl.ubc.ca Lectures: M,W,F 13:00-13:50 Tutorials: Tu 14:00-15:30 Room: 307 West Mall Swing Space Room: 153 Friedman Building website: http://blogs.ubc.ca/biol433/http://blogs.ubc.ca/biol433/

2. Reading: A. Papers and reviews to be downloaded. B. Selected parts available for purchase at the UBC Bookstore for the following texts: Westhoff et al. 1998. Molecular Plant Development: From gene to plant. Oxford University Press, Oxford. Useful for some topics; Buchanan et al. 2000. Biochemistry & Molecular Biology of Plants. American Society of Plant Physiologists, Rockville MD. Book chapter on SA and SAR by Terry Delaney

3. Lecture outline: A.Basic information and methods in plant genetics (10 lectures) Plant genomes and genomics (Haughn) Classical and molecular genetics: mutants; gene mapping, cloning and molecular analysis (Haughn, Kunst) Gene transfer in plants (Kunst) Reverse genetics (Li) B. Topics in plant genetics (26 lectures) Biochemistry and metabolism (Kunst; 8 lectures) Development (Haughn; 9 lectures) Plant-pathogen interactions (Li; 9 lectures)

4. Tutorials A paper will be assigned for each of 12 tutorials (paper on web) The paper topics relate to the lecture material. You should read 'Tips for Reading a Paper'.Tips for Reading a Paper Assignments for individual tutorials will direct your attention to important points in each paper. All tutorials except for the first two will be student-led. DateTopic Activity ____ Jan. 8Molecular analysis of plant genes class discussion Jan. 15Genomicsassignmentclass discussion Jan. 22biochemistry assignmentgroup presentation Jan. 29biochemistry ““

5. Evaluation 35% Final exam 30% Take-home problem assignments (3). 10% Tutorial assignments (10) 20% Tutorial presentation (group presentations of tutorial papers, including an individual written report) 5%Class participation

6. Tutorial Presentations You will be evaluated on the quality of your presentation as a group (5%) and individually (10%) for oral presentation. + 5% for your own written summary of the paper for a total of 20% of the course mark.

7. Lecture 1: Plant Genomics Objectives: 1.Why sequence a genome? 2.Which multicellular organisms were sequenced first. Why were they chosen? 3.How are genomes sequenced? 4.What do we learn from sequencing a genome? What do we not learn?

8. Lecture 1 Assigned Reading: Somerville, C.R. and Somerville, S.C. 1999. Plant Functional Genomics. Science 285:380-383. Buchanan text. Chapter 7. References: The Arabidopsis Genome Initiative. 2000. Analysis of the Genome Sequence of the flowering Plant Arabidopsis thaliana. Nature 408: 796-815. Berardini et al., 2004. Functional Annotation of the Arabidopsis Genome. Plant Physiology 135: 745-755.

9. Why sequence genomes? The genome sequence provides:

10. Why sequence genomes? The genome sequence provides: --accurate genome size --number and type of genes. --gene/genome structure (splice junctions, base composition, gene spacing, redundancy) --tools for investigating gene function.

11. Genome Sequence of Multicellular Organisms First completed for: Caenorhabditis elegans1998 Drosophila melanogaster2000 Arabidopsis thaliana2000 Why were these organisms chosen?

12. Genome Sequence of Multicellular Organisms First completed for: Caenorhabditis elegans1998 Drosophila melanogaster2000 Arabidopsis thaliana2000 Why were these organisms chosen? Small size Large number of progeny Short generation time Small genome (50-150 Mbp) Studied genetically for many years

13. How were these genomes sequenced? 1.Create a library of large genomic fragments for organism of interest. (eg bacterial artificial chromosomes (BAC vector takes 100-200 kb fragments of genomic DNA).

14. Isolated genomic DNA contains many copies of each chromosome (from many cells) Shear randomly into large pieces Ligate fragments into a BAC vector ( )

15. How were these genomes sequenced? 1.Create a library of large genomic fragments for organism of interest. (eg bacterial artificial chromosomes (BAC vector takes 100-200 kb fragments of genomic DNA). 2.Place BAC clones into contigs (contiguous DNA segments) by sequencing a few (500) clones (seed BACs) completely and sequencing only the ends of many more clones (10,000). Use a computer to match the end sequences to the seed clones to group and align the BAC clones.

17. How were these genomes sequenced? (cont.) 3.Choose the minimum number of clones (minimum tiling path) to cover as much of the the entire genome as possible

19. How were these genomes sequenced? (cont.) 3.Choose the minimum number of clones (minimum tiling path) to cover as much of the the entire genome as possible. 4.Sequence the BACs in the minimum tiling path. Contigs can be linked by identifying a clone that spans two contigs.

21. New Generation Sequencing Techniques Illumina (Solexa) Roche (454) Applied Biosystems Inc. (SOLiD system) Shotgun sequencing many fragments in parallel. Nature Methods - 5, 16 - 18 (2008) http://www.nature.com/nmeth/journal/v5/n1/full/nmeth1156.html

22. Information obtained from sequencing the Arabidopsis genome Genome size: 115 Mbp sequenced + 10 Mbp highly repetitive: (rDNA, Centromere) = 125 Mbp Sequence is 99.99% accurate

23. Annotation Identification of genes: How? Use known sequence features of genes to predict: Open reading frames, Splice junctions, promoter elements, base composition, translation initiation sites. Refine with cDNA sequence. Predict: Arabidopsis 27,000 (estimates) C. elegans19,000 D. melanogaster14,000

24. Redundancy Arabidopsis is an ancient tetraploid Segmental duplications of the chromosomes are extensive (60%) Organism #genes #gene families %genes with or unique genes unique sequence (singletons) Arabidopsis 27,000 12,00035% C. Elegans19,00014,00055% Drosophila14,00010,00072%

25. Gene function Define gene function on the basis of Biochemical role Based on sequence similarity to known proteins Biological process? Cellular function? Plant Functional Genomics Chris Somerville* and Shauna Somerville. 1999 SCIENCE VOL 285 + 900 non-coding