Lecture 14: Genes and Genomes

what is a gene

region of DNA coding either for the messenger RNA encoding the amino acid sequence in a polypeptide chain or for a functional RNA molecule

the _____ is the complete set of genetic material in an organism

genome

dna in most organisms is compacted at multiple scales into _______

chromosomes

ploidy

number of copies of each chromosome in an organism

humans are diploid which means…

two copies of each chromosome

polyploidy

duplications of the entire genome

genomes are messy outcomes of what?

cooperation and conflict, mutation, selection, and drift

viruses and prokaryotes have nearly ____ coding DNA

100%

selection to _________ is intense in rapidly dividing microbes that have large population sizes

maintain a minimal genome

plants and animals are made largely of _____ DNA

noncoding

selection for genome streamlining is _____ in most euklaryotes

absent

only ___ of the human genome is made up of protein coding genes

2%

_____ of the human genome is made up of selfish genetic elements (DNA parasites like transposable elements)

50%

what are transposable elements

self-cutting / copying DNA elements

• example: Alu proliferates by making copes of itself

Alu elements make up _____ of the human genome

>10%

Alu elements do not reproduce because they improve our fitness, so why?

simply because they can

each of us has more than _____ copies of Alu elements

10^6

Alu elements often cause a ____ in fitness

decrease

insertion of selfish elements into genes or regulatory regions can do what?

alter or stop gene expression

copies of elements in different parts of the genome can do what?

recombine and cause chromosomal mutation

new genes most often evolve by ….

reshaping old genes for new function

crystallin

a protein in that occurs in vertebrate eyes and allows them to focus light

3 main ways in which new function functions can evolve in the genome:

1. gene duplication and divergence

2. introgression and horizontal gene transfer

3. de novo gene evolution

pseudogenization

genes also go through a process of death in which the functional processes of a gene are lost over time (happens when selection is not maintaining function)

____ is the most common way that new genes arise in eukaryotes

duplication

gene duplication

the process in which a gene, genome region, or a whole genome getting duplicated

paralogs

Genes that originated by duplication

Copy number variation

when there is polymorphism in the number of copies of the gene that individuals carry

Once there are two copies of a gene, their functions can diverge so that …

one of the copies takes on a novel function

Phylogenies of genes can do what?

give us a detailed account of the evolutionary history a gene (descent with modification – just like species)

genes have gone through multiple rounds of duplication to form a ‘gene family’, which is ….

a related set of genes that evolved from a common ancestor

What are the molecular mechanisms of gene duplication?

• replication slippage

• unequal crossing over

• retro-transposition

• whole genome duplication

Replication slippage

• DNA polymerase ‘loses its place’ and copies a segment of a chromosome twice

• Causes tandem repeats (copies of a gene that are right next to each other

Unequal crossing over

• recombination occurs between different portions of a chromosome that are misaligned during meiosis

• Can be enhanced by the presence of transposable elements which cause chromosomes to misalign

• causes tandem repeats

Retro-transposition

• A gene gets reverse transcribed from an mRNA and then gets reinserted elsewhere in the genome

• Repeats are not tandem

• Duplicates lack introns

Whole genome duplication

• Every gene and noncoding portion of the genome gets duplicated

• Can occur if the genome of a single species is duplicated (through an error in meiosis) – Autopolyploidy

• Can occur through a hybridization event between species in which each contributes their whole complement of chromosomes to the hybrid species – Allopolyploidy

what happens to duplicated genes

1. subfunctionalization

2. neofunctionalization

3. pseudogenization

4. maintenance

Sub-functionalization (Force 1999)

• Each of the copies evolves deleterious/neutral mutations that causes divergence.

• Complementary deleterious mutations occur in each copy of the gene and subdivided functions of the original gene are selected in each copy.

• This model is often favored since it does not require any beneficial mutations.

Neo-functionalization (Ohno 1970)

• Duplication of a gene occurs, one of the copies retains the original function, and the other copy (released from selection to maintain the original function) evolves a new function.

• requires the occurrence of beneficial mutations favoring the adaptive evolution of novel function

When a gene is duplicated, the new copy is often not necessary. The duplicate may ….

not include the entire gene, lack introns, or lack the regulatory elements needed to express it.

Because the pseudogene does not produce a functioning product, it is freed from _______________ and will accumulate mutations

purifying selection (selection against deleterious mutations)

A duplicate can also simply _____

retain its original function

Duplicates can be favored to continue functioning when there is ….

selection for increased expression of the gene’s product.

Introgression

the transfer of genetic information from one species to another as a result of hybridization and repeated backcrossing

Horizontal gene transfer (HGT)

nonreproductive passage of genes among organisms

____ is particularly important to prokarytotes, and is the most common way by which they acquire new genes, including those that confer antibiotic resistance

horizontal gene transfer (HGT)

De novo genes have evolved from noncoding DNA

• this could occur is if a mutation in a noncoding region by chance turns on the expression of some downstream DNA

• This explains orphan genes, which expressed genes that are only found in single species (no evidence of homology in related species)

• New data from sequencing genomes of related populations of Drosophila uncovered an average of 49 de novo genes per species, many expressed in testes