Genomes and Their Evolution Chapter 18 Genomes and Their Evolution

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.

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

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

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

Comparing Genomes of Bacteria, Archaea, & Eukaryotes

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

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

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

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

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

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

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

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

Transpositions  Chromosomal Rearrangements

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

HHMI Short Film: The Birth & Death of Genes

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

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

Video Clip: What are SNPs?

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

Conservation of homeotic genes