Download BIOL 433 Plant Genetics Term 1, 2005

BIOL 433 Plant Genetics
Term 2, 2015-2016
Instructors:
Dr. George Haughn
BioSciences 2239
822-9089
[email protected]
Dr. Ljerka Kunst
BioSciences 2237
Tel. 822-2351
[email protected]
Dr. Yuelin Zhang
Biosciences 2207
(604) 827-3794
[email protected]
Lectures: M,W,F 13:00-13:50
Room: 207 Neville Scarfe
website: http://blogs.ubc.ca/biol433/
Tutorials: Tu 14:00-15:30
Room: 201 Hugh Dempster Pavillion
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:
A. Basic information and methods in plant genetics (9
lectures)
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•
•
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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)
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•
•
Biochemistry and metabolism (Kunst; 9 lectures)
Development (Haughn; 9 lectures)
Plant-pathogen interactions (Zhang; 9 lectures)
Tutorials
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•
•
•
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
• Jan. 12
Topic
Molecular analysis of plant genes
Activity
____
class discussion
• Jan. 19
Genomics
assignment
class discussion
• Jan. 26
biochemistry
assignment
group presentation
• Feb. 2
biochemistry
“
“
Evaluation
35%
30%
10%
20%
5%
Final exam
Take-home problem assignments (3).
Tutorial assignments (10)
Tutorial presentation (group presentations of
tutorial papers, including an individual written report)
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:
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?
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?
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).
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?
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.
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:
(estimates)
Arabidopsis
C. elegans
D. melanogaster
27,000
19,000
14,000
Redundancy
Arabidopsis is an ancient tetraploid
Segmental duplications of the chromosomes are extensive
(60%)
Organism
#genes
#gene families
or unique genes
%genes with
unique sequence
(singletons)
Arabidopsis
C. Elegans
Drosophila
27,000
19,000
14,000
12,000
14,000
10,000
35%
55%
72%
Gene 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?