Genomes and their evolution

1
Genomes and their evolution

• How do we study genomes?
• What can we learn from them?

2
Why study genomes?

• We can look at similarities and differences
• We can learn more about gene interaction and
  control of gene expression
• We can learn more about the history of life on
  Earth
• Genomics the study of whole sets of genes and
  their interactions within a species, as well as
  genome comparisons between species
• BioinformaticsThe use of computers, software,
  and mathematical models to process and integrate
  biological information from large data sets
• Dependent on technological advances!

3
How do you sequence a genome? Human Genome Project

• Built on previous technologies
• Linkage map the order of markers through the
  chromosomes
• Physical maps how far apart are the markers?
• Sequencing break up DNA into pieces and sequence
  them

4
Shotgun approach Venter and Celera

• Competed with hierarchical approach
• Competition probably hastened completion of
  sequencing
• Metagenomics sequences from organisms within a
  specified environment

5
Bioinformatics you have all that data, what do
you do with it?

• Databases and centers
• National Center for Biotechnology Information
• NCBI houses Genbank
• BLAST allows sequences to be compared
• Predicted amino acids sequences comparison to
  others
• Comparions can be useful for gene identification
• Other centers around the world

6
What does bioinformatics look like?
7
ENCODE ushered in the approach of studying DNA-
protein interactions
8
What do we learn by comparing genomes? Introns
primarily a feature of eukaryotes, as
is noncoding DNA What does this mean?
9
Significance of noncoding DNA?

• Most is repetitive DNA
• Transposable elements
• Almost half the human genome
• Unique noncoding pseudogenes

10
Transposons

• DNA intermediates
• May be excised and moved, or copied and moved

11
Retrotransposons

• May be origin of reverse transcriptase
• Alu elements
• LINE-1 retrotransposons
• LINE long interspersed nuclear element
• SINE short
• ERV endogenous retroviruses
• LTRs long terminal repeats
• May include promoters and enhancers

12
STRs short tandem repeats

• 2 to 5 nuleotides
• Actual number of repeats can vary in individuals
• Tends to be at centromeres and telomeres
• May have stabilizing effect

13
(Multi)Gene families

• Collection of two or more related genes
• Identical to make many copies of an essential
  protein (like rRNA)
• Non-identical different versions of a protein
• Developmental significance?

14
How does genome evolve?

• Mutation
• Duplication
• Alteration of structure
• Some regions are conserved among species
• Might contribute to speciation
• Some sites are more susceptible to mutation than
  others

15
How does duplication occur?
16
A model for evolution of gene families
17
Exon shuffling production of novel proteins

• Typically, exon shuffling produces different
  versions of proteins
• Can lead to formation of new genes
• Transposable elements may be responsible for
  arrangement of genes on chromosomes

18
What can be learned by comparing genome sequences?

• When did species diverge?
• What are their common genes?
• Variation within a species
• Closely related species which regions are
  stable, which have changed rapidly?
• Study genes associated with species differences

19
Conservation of developmental genes

• homeodomain (regulatory sequence)
• Hox genes contain this region
• Generally associated with development
• Changes can affect body plan
• Regulatory sequences very different in plants

20
Conservation of developmental genes

• homeodomain (regulatory sequence)
• Hox genes contain this region
• Generally associated with development
• Changes can affect body plan
• Regulatory sequences very different in plants

21
Summary

• Genomics and proteomics are rapidly developing
  fields
• Bioinformatics allows for the analysis of genomes
  and proteins in a system-wide approach
• Genomes vary widely among organisms
• Eukaryotic genomes are complex and have much
  noncoding DNA
• Comparing genomes gives insights into evolution
  and development