Chapter 21 Genomes and Their Evolution Bioinformatics Use

Chapter 21 Genomes and Their Evolution

Bioinformatics Use of computers, software, and math models to process and integrate data from sequencing projects

Human Genome Project Purpose: to sequence the entire human genome Completed in 2003 Genomes sequenced thus far*: 58, 000 prokaryotes, 2700 eukaryotes, 5300 viruses * Data as of 1/27/16

Human Genome Project

Comparing Genomes of Bacteria, Archaea, & Eukaryotes

Human DNA • 3 billion base pairs • ~20, 000 genes • Only 1. 5% codes for proteins (or RNA) • Mostly Repetitive DNA: DNA sequences present in multiple copies

Video Clip: What are SNPs?

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 Mc. Clintock – 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

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: fish old protein gene transformed into a new gene with new structure/function Gene mutates duplicated divergent evolution

Evolutionary Development (Evo-devo) • Compares developmental processes to understand how changes can lead to evolution of organisms

Homeotic genes: genes master regulatory genes • Control placement and spatial organization of body parts Homeobox: Homeobox widely conserved 180 -nucleotide sequence within homeotic (Hox) genes • Found in many groups (fungi, animals, plants) • Hints at relatedness between all life forms

Conservation of homeotic genes