Introduction to Genomics

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• Introduction to Genomics

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Post genomics ?Knowledge of the function of a
genome

• What is genomics ?
• Knowledge of the whole genome of an organism

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• Why sequence a genome ?
• How do you sequence a genome ?

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• Many organisms have now been sequenced

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• A new sequencing project
• How would you start ?

Rapid lifecycle Apomyctic Commercial
interest Transgenics ? Genome size ? Linkage
groups ? Funding ?
Slow lifecycle Can be cloned Commercial
interest Transgenics ? Genome size ? Linkage
groups ? Funding ?
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• Practical step 1.
• Do you have a model framework to fix your
  genome on ?
• Synteny

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Crop circles
Gale Devos
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Cat vs human synteny
Why cats ?
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Human/Mouse Synteny
-The order of genes within eachblock of DNA is
conserved in different species even though the
blocks have assembled to give vastly different
numbers length of chromosomes
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• - orientation of genes are conserved too
• - Gene pairs that are syntenic are most likely
  orthologous (direct evolutionary counterpart
  Related by vertical descent)

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Human/mouse synteny (gene level)
- Gene structures such as regulatory regions,
splice sites, exon number, exon length and
sequence similarity (DNA and protein level) tend
to be more conserved - Intronic sequences and
length tend to be less conserved
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• Step 2.
• Map your genome
• Genetic maps
• Physical maps

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Arabidopsis recombinant inbred maps micro-linkag
e groups Made from the performance or markers
across 2-300 lines
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• Step 3.
• Break your genome up into manageable fragments
• YAC
• BAC
• Cosmids
• ESTs (expressed sequence tags)

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STS (sequence tagged site) Short (200 to 500 bp)
DNA sequence that has a single occurrence in the
genome and whose location is known.
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Minimal tiling path
BAC tiling path - mouse
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• Sequence the bitsOld fashioned. -OR-
  next-gen e.g. Solexa or 454
• Stick on ESTs to show regions of genes
• Analyse by example (training sets) to develop
  in-silico predictions of unknown genes.

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• Global analysis
• What does the genome look like ?

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What do the genes do ?