Lecture #14 | Genes and Genomes

Flashcards on Genes and Genomes

Gene

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

Proteins

Perform most biological functions in organisms

• transport

• enzymes

• hormones

• antibodies

Genome

The complete set of genetic material in an organism

• very small amount of genome is actually coding

Ploidy

The number of copies of each chromosome in an organism

Humans are diploid: two copies of each chromosome

Polyploidy

Duplications of the entire genome.

Transposable elements

Self-cutting/copying DNA elements.

• ex: Alu

The DNA sequence is transcribed into RNA which is then reverse transcribed back into DNA and inserted somewhere else

• copy + paste mechanism

Gene duplication

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

• Most common way that new genes arise in eukaryotes

Paralogs

Genes that originated by duplication.

Replication slippage

Molecular mechanism of gene duplication

DNA polymerase ‘loses its place’ and copies a segment of a chromosome twice, causing tandem repeats.

Unequal crossing over

Molecular mechanism of gene duplication

Recombination occurs between different portions of a chromosome that are misaligned during meiosis, causing tandem repeats.

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

Retro-transposition

A molecular mechanism of gene duplication

A gene gets reverse transcribed from an mRNA and then gets reinserted elsewhere in the genome; duplicates lack introns and are not tandem.

Whole genome duplication

Molecular mechanism of gene duplication

Every gene and noncoding portion of the genome gets duplicated.

Sub-functionalization

One option of what occurs to duplicated genes

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.

Model is often favored since it does not require any beneficial mutations

Neo-functionalization

One option of what occurs to duplicated genes

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.

Pseudogene

Option for what happens to a duplicated gene

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.

• does not produce a functioning product, it is freed from purifying selection and will accumulate mutations

• the cause of DMIs in rice lineages

Introgression

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

• can lead to new genes from another species

Horizontal gene transfer (HGT)

Nonreproductive passage of genes among organisms

• can lead to new genes from another species

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

Orphan genes

Expressed genes that are only found in single species (no evidence of homology in related species)

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

Locus

The specific physical location of a gene or other DNA sequence on a chromosome, like an address. A variant at a locus is called an allele.

do RNA have to be translated to have a function?

Yes, RNA can have multiple functions even if not translated into protein that perform 2ndary functions

Chromosome

DNA is packed into chromosomes

extracellular DNA is not arranged in chromosomes

Do all large organisms always have larger genomes that small, simple organisms?

No, not necessarily

• no relationship between amount of DNA an organism has compared to it size

Genomes are messy outcomes of cooperation & conflict,

mutation, selection, and drift

Do large, complex organisms have more genes than

small, simple organisms?

No, more complex organisms do not always have more genes

• Organisms without different tissues tend to have fewer genes

• but some plants and animals have an extraordinary number of genes

How does coding and non coding (genome content) vary across the diversity of life?

Viruses and prokaryotes have nearly 100% coding DNA while Plants and animals are made largely of concluding DNA

• In viruses, selection to maintain a minimal genome is intense in rapidly dividing microbes that have extremely large population size

• In plants/animals: selection for genome streaming is absent in most eukaryotes

What % of human genome is made up of protein coding genes?

2%

• 50% of the human genome is made up of selfish genetic elements (like transposable elements)

• ex: Alu elements

Alu elements

A selfish DNA parasite that make up >10% of human genome

• about 300 basepairs long and proliferate by making copies of themselves

• reproduce because they can, not because they improve our fitness

• each of us has 10^6 copies of Abu elements

  • Often can decrease fitness

  • Insertion of selfish elements into genes or regulatory regions can alter or stop gene expression

How do new genes evolve?

By reshaping old genes for new function

1. gene duplication and divergence (most common way that new genes arise in eukaryotes)

2. Intorgression and horizontal gene transfer

3. De novo gene evolution

pseudogenization

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

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.

• represents a fast-evolveing aspect of human evolution

How can we know that a gene has duplicated and diverged within a genome?

We can use phylogenies of genes

• give a detailed account of the evolutionary history of a genes

• Sometimes, multiple rounds of duplication form a gene family; a related set of genes that evolved from a common ancestor

Autopolyploidy

molecular mechanisms of gene duplication

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

Allopolyploidy

molecular mechanisms of gene duplication

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

What happens to duplicated genes?

4 options

1. Subfunctionalization

2. Pseudoginzation

3. Neofunctionzatization

4. Maintenance

Maintenance of duplicated genes

Duplicate retains original function

• can be favored to continue functioning when there is selection for increased expression of the gene’s product

• ex: many insects have evolved resistance to pesticides via gene duplication. Duplicates of those genes are favored because they increase gene expression and so enable the insect to detoxify the pesticide more rapidly

Copy number variation in humans with AMY1

Codes for amylase, enzyme in the saliva that breaks down starch

• humans with more than one copy of AMY1 can digest starch more efficiently because they have more products of the gene

• human populations vary greatly in terms of how many copies of AMY1 they have and this is largely driven by diet

  • in cultures that eat a lot of starch, individuals can have as many as 15 copies of AMY1

How is horizontal gene transfer related to the bird-flu epidemic?

50-100 million people died because of a viral gene transfer between a human influenza virus and a bird flu virus that exhibited severe virulence in the human host

How have de novo genes evolved from noncoding DNA?

A mutation in a noncoding region by chance turns on the expression of some downstream DNA

• explains orphans genes