1. Genomes and Their Evolution
Chapter 18
Genomes and Their Evolution

2. What you need to know: The major goals of the Human Genome Project.
How prokaryotic genomes compare to eukaryotic genomes.
Applications of bioinformatics to medicine, evolution, and health.
The activity and role of transposable elements and retrotransposons in generating genetic diversity.
How evo-devo relates to our understanding of the evolution of genomes.
The role of homeotic genes and homeoboxes in developmental patterns and sequences.

3. Bioinformatics
Use of computers, software, and math models to process and integrate data from sequencing projects
Genomics: study whole sets of genes and their interactions
Proteomics = Analyzing protein interactions

4. Human Genome Project Purpose: to sequence the entire human genome
Completed in 2003
Genomes sequenced thus far*: 129,936 prokaryotes, 5102 eukaryotes, 14,004 viruses
*NCBI database as of 1/23/18

5. Whole-genome shotgun approach to sequencing
Human Genome Project
Whole-genome shotgun approach to sequencing

6. Comparing Genomes of Bacteria, Archaea, & Eukaryotes

7. Comparing Genomes Bacteria & Archaea have fewer genes than eukaryotes
No correlation between complexity of organism and # of genes

8. Human DNA 3 billion base pairs ~20,000 genes
Only 1.5% codes for proteins (or RNA)
Mostly Repetitive DNA: sequences present in multiple copies

9. Transposable Elements
Make up 75% of repetitive DNA
Stretches of DNA that can be moved from one location to another in genome
Discovered by Barbara McClintock – corn breeding experiments
2 Types:
Transposons
Retrotransposons

10. Transposons Moves within genome via DNA intermediate
“cut & paste” or “copy & paste” mechanisms
Requires enzyme transposase

11. Retrotransposons Move by means of RNA intermediate
Leaves copy at original site
Involves enzyme reverse transcriptase

12. Other Repetitive DNA Short Tandem Repeat (STR)
Repeating units of 2-5 nucleotides
# of copies varies from site to site
Repeats vary from person to person  unique set of genetics markers
Genetic profiles created by STR analysis

13. Genome Evolution Insertion effects of transposons:
Can interrupt or alter gene function
Multiple copies of genes
Duplication  genes with related functions
Genes diverge by accumulating mutations
Some become nonfunctional pseudogenes
Eventually, new genes with new functions can occur

14. Multigene Families
Collections of 2 or more identical or very similar genes
Eg. hemoglobin: -globin and -globin gene families

16. Transpositions  Chromosomal Rearrangements

17. Transposable elements contribute to evolution
Promote recombination, disrupt genes or control elements, & carry genes to new locations
May be harmful or lethal, but can also have small beneficial effects
Provides raw material for natural selection

18. HHMI Short Film: The Birth & Death of Genes

19. Illustrative Example: Antifreeze Gene in Fish
Antifreeze proteins (AFP): produced by vertebrates, plants, fungi, bacteria to aid survival in sub-zero environments
Function: bind to ice crystals and prevent growth
Antarctic fish: old protein gene transformed into a new gene with new structure/function
Gene mutates  duplicated  divergent evolution

20. Evolutionary Development (Evo-Devo)
Compare developmental processes to understand how changes can lead to evolution of organisms

21. Video Clip: What are SNPs?

22. Homeotic Genes: master regulatory genes
Codes for transcription factors
Control placement and spatial organization of body parts by controlling developmental fate of groups of cells
Homeobox: widely conserved 180-nucleotide sequence within homeotic (Hox) genes
Found in many groups (fungi, animals, plants) with very few differences
Hints at relatedness between all life forms

23. Conservation of homeotic genes