Transcript Genome Analysis

Genome Analysis
Assaad
text book slides only
Lectures by F. Assaad can be downlaoded from
http://www.botanik.biologie.tumuenchen.de/~farhah/index.htm
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.
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
Fingerprint
(restriction digest
separated on gel)
of BAC clones
DNA fingerprints can be
used to align
BAC clones.
In addition, 18,300 BAC end
sequence reads were used to
generate a physical map.
Sequencing of ordered clones
Science 2002. 296: 61.
Scrambled
blocks of genes
in common between
the human and
the mouse.
Text Book Readings
• Modern Genetic Analysis Integrating genes
and genomes 2nd edition. Giffiths and Lewontin
Chapter 4 Mitosis vs Meiosis
Chapter 6 Recombination, Linkage
Chapter 9 Genomics
For next lecture see pages 303-305.
• Genes VIII, Benjamin Lewin ISBN 013144946X
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)
Vocabulary
• PCR, meiosis, recombination, segregation (should know)
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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
October 24th
Assaad
Genome Analysis
November 14th
Gierl
Transcriptome, Proteome, Metabolome
November 21st
Grill
Gene Identification
November 28th
Assaad
Forward versus Reverse Genetics
December 5th
Assaad
Vesicle Traffic, Cell Wall
December 12th
Assaad
Functional Interactions
December 19th
Grill
Gene Structure
January 9th
Grill
Gene Expression, Regulation 1
January 16th
Grill
Protein Modifications, Regulation 2
January 23rd
Grill
Signaling
January 30th
Assaad
What we have learnt