BIOL 433 Plant Genetics Term 2, 2015-2016 Instructors: Dr. George Haughn Dr. Ljerka Kunst BioSciences 2239 BioSciences 2237 822-9089 Tel. 822-2351 george.haughn@ubc.ca ljerka.kunst@ubc.ca Dr. Yuelin Zhang Biosciences 2207 (604) 827-3794 yuelin.zhang@ubc.ca Lectures: M,W,F 13:00-13:50 Tutorials: Tu 14:00-15:30 Room: 207 Neville Scarfe Room: 201 Hugh Dempster Pavillion website: http://blogs.ubc.ca/biol433/

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

Lecture outline: Basic information and methods in plant genetics (9 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 (Zhang) B. Topics in plant genetics (27 lectures) Biochemistry and metabolism (Kunst; 9 lectures) Development (Haughn; 9 lectures) Plant-pathogen interactions (Zhang; 9 lectures)

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'. 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. Date Topic Activity ____ Jan. 12 Molecular analysis of plant genes class discussion Jan. 19 Genomics assignment class discussion Jan. 26 biochemistry assignment group presentation Feb. 2 biochemistry “ “

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

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.

Lecture 1: Plant Genomics Objectives: Why sequence a genome? 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?

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.

Why sequence genomes? The genome sequence provides: -mutations -compare within and between species -all genes in a genome -regulatory sequences -genome size -gene arrangement

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) --sequence polymorphisms for evolutionary studies. --tools for investigating gene function.

Genome Sequence of Multicellular Organisms First completed for: Caenorhabditis elegans 1998 Drosophila melanogaster 2000 Arabidopsis thaliana 2000 Why were these organisms chosen? -small genome size. -short life cycle -easy to grow in lab small -cheaper

Genome Sequence of Multicellular Organisms First completed for: Caenorhabditis elegans 1998 Drosophila melanogaster 2000 Arabidopsis thaliana 2000 Why were these organisms chosen? Small size Large number of progeny Short generation time Small genome (50-150 Mbp) Studied genetically for many years

How were these genomes sequenced? 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).

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

How were these genomes sequenced? 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). 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.

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

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.

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

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

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. elegans 19,000 D. melanogaster 14,000

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 12,000 35% C. Elegans 19,000 14,000 55% Drosophila 14,000 10,000 72%

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