genomes and evolution

Question 1

Brief history of genome discoveries (19th to mid-twentieth century)

Answer 1

Gregor Mendel (1822-1884)
Showed units of inheritance are discreet, don’t blend, and persist overtime
Used this concept to predict the phenotype of pea plants

Law of segregation: the two alleles at a(diploid) locus separate during the process of forming gametes (meiosis), and randomly unite at fertilisation (in the zygote)

Law of independent assortment: the two alleles separate independently during the formation of gametes, so that traits are transmitted to offspring independent of each other

Reginald C. Punnett (1905)
Introduced the punnett square in 1905

Thomas Hunt Morgan (1866 –1945)
Nobel Prize in Physiology and Medicine 1933 for discoveries relating the role the chromosome plays in heredity

through his studies of mutations in fruit flies he demonstrated that genes are carried on chromosomes and are the mechanical basis of heredity

In particular, showed in 1911 that the white-eye mutant in Drosophilla was sex linked, and inferred the link to chromosomes from that.

Frederick Griffith (1928)

Non-virulent bacteria injection – mouse survives
virulent bacteria injection – mouse dies
virulent bacteria killed by heat – mouse survives
Non-virulent bacteria + heat treated virulent injection – mouse dies – as bacteria can transfer DNA from one to the other

Oswald Avery (1877-1955)

Built on the work by Frederick Griffith

Showed that DNA is the ‘transforming principle’, and that the polysaccharide coat of a bacterium was not – by testing isolated components of the cell in transformation experiments (Avery et al. 1944).

James Watson & Francis Crick (1953)

building on the X-Ray crystallography work of Rosalind Franklin and Maurice Wilkins determined the double-helix structure of DNA in 1953

Question 2

The composition and nature of nuclear genomes

Answer 2

Nuclear genomes vary a great deal in size, and are divided into chomosomes in eukaryotes.

Weight of genome corresponds to number of chromosome pairs and hence to genome size

There are likely many reasons for variation in genome size, but one correlation within taxa is with body size.

->See: Gregory et al. (2000). Evolutionary implications of the relationship between genome size and body size in flatworms and copepods. Heredity 84: 201-208.

However, beyond specific taxa, this relationship breaks down

Question 3

Non-coding DNA

Answer 3

Much of non-coding DNA is repetitive

Protein coding genes make up just 1.5% of the human genome and this is similar throughout eukaryotes

Question 4

Genome sequencing

Answer 4

In 2001 the first draft of a full genome was compiled it was actually only 90% of it. This took years to do, a whole building full of machines and ~billions of dollars

In 2010 the 1000 genome project was carried out

In 2018 the 100,000 genome project was completed in the UK and 1 million had been sequenced world wide – the technology had improved rapidly

However these genomes tended to have gaps where repetitions were missed etc.

Now it is possible to sequence whole genomes using telomere to telomere (T2T) technology

The first human genome to be sequenced using T2T was in 2022

-> See - Nurket al. (2022) Science 376,44–53 : The first gapless, complete human genome

Currently the Earth biogenome project is trying to sequence the 1.5 million different eukaryote genomes, they have sequenced nearly 2000 species so far.

Question 5

What is the rest of the genome doing if it is not coding?

Answer 5

Scientists were looking at RNA transcription and observing the different parts of the genome that produce RNA to see if non-coding regions were governing transcription

Discovered that 75% of the genome is producing RNA

Encode Project came together to look at the different classes of RNA products being produced

See: www.pnas.org/cgi/doi/10.1073/pnas.1318948111

Also see Encode project website

Question 6

According to the Encode project: It seems that a lot of the RNA being produced is micro RNA (miRNA)

Answer 6

Micro RNA: ~22 nucleotides long, regulates gene expression at post-transcriptional level (development, apoptosis, metabolism)

Scientists were looking at RNA transcription and observing the different parts of the genome that produce RNA to see if non-coding regions were governing transcription

Discovered that 75% of the genome is producing RNA

Encode Project came together to look at the different classes of RNA products being produced

See: www.pnas.org/cgi/doi/10.1073/pnas.1318948111

Question 7

Dan Graur disagreed with this 75% functional theory

Answer 7

Mutational load: whenever there is a mutation that affects the gene there is a potential negative effect

If mutational load is considered this leads to the conclusion that the functional fraction within a human genome cannot exceed 25% and is likely much lower than this

So yes some proportion of the genome functions alongside the genes to regulate them

However there is still a lot of so called ‘junk’ that we currently do not know its purpose

Some of it is probably architectural whereas other areas are likely to be repetition

Question 8

The composition and structure of organelle genomes

Answer 8

Consistently ~17000 Kb in mitochondrial DNA in eukaryotes ~1Kb non-coding ‘controller region’

Mitochondrial and chloroplastic DNA is far more complicated and variable than in eukaryotes

Question 9

How do genomes change over time? (1)

Answer 9

Triplet codons code for different aminos though some aminos have more than one codon that code for them

Insertion and deletion cause frame shifts – changing all the aminos coded after them

Genes also contain non-coding areas ‘residues’ that can change without affecting the amino produced

Mutation rate tends to be proportional to the overall population size of the species

Lower in larger populations

Many potential causes of mutation e.g. UV light

Question 10

How do genomes change over time? (2)

Answer 10

Across taxa and within genomes many different mutations can occur

Areas of high levels of mutation are known as ‘hot spots’

No mutation = synonomous change (equivalent substitution)

Silent = no visible phenotypic effect

Nonsense = stop codon

Missense =

conservative – doesn’t cause much change in the protein shape

or nonconservative – does cause a change in protein shape

Transition – change from one pyrimidine to another or one purine to another – usually faster

Transversion – change from a pyrimidine to a purine or vice versa

Question 11

Repetitive DNA

Answer 11

simple repeats make up about twice as much of vertebrate nuclear genomes as single-copy coding genes.

Makes up a lot of the genome

Often referred to as satellite DNA because it collected at a separate peak on a centrifuge gradient as a ‘satellite’ to the distribution

Tandem repeats of 100s or 1000s of up to ~500bp motifs

Question 12

Satellite DNA

Answer 12

named for the segregation of a lot of similar sized DNA on a centrifuge gradient as a ‘satellite’ to the distribution

Mini satellite DNA
named this because the length of the repeat arrays was shorter than for ‘satellite DNA’ arrays

Alec Jeffries developed the technique of ‘DNA fingerprinting’ after discovering these highly variable, mini-satellite DNA arrays – a way to identify individuals

Micro-satellite DNA
Repeat arrays that are even shorter and simpler than mini-sattelites

Deithard Tautz first published on this type of locus, which later became the marker of choice for forensic work previously done by mini-satellite ‘DNA fingerprinting’

Identifiable on a gel and vary greatly

Repetitive DNA aka satellite DNA evolves very quickly via DNA turnover mechanisms that generate variation in the length of repeats.

Question 13

Gene families

Answer 13

These are repetitive arrays of genes e.g. ribosomal DNA (rDNA) repeats a lot as it is essential for coding large quantities of it

Question 14

DNA turnover mechanisms

Answer 14

DNA Slippage – within chromatids or during replication

Unequal Crossing-over – within repetitive non-coding arrays, or within gene families

Gene Conversion – promoting greater or less diversity

Transposition – ‘Jumping genes’

Question 15

DNA slippage

Answer 15

within a single chromatid:
a combination of strand breakage, looping and repair could lead to expansion (repeat array) or contraction

slippage during replication:
misalignment within the array during replication together with excision or repair leading to expansion or contraction

Question 16

Unequal crossing over

Answer 16

within repetitive non-coding arrays:
due to misalignment

or within gene families:
at IGS sub-repeats or at the level of rDNA in tandem array leading to variation in no. of whole rDNA units and can spread variation at the level of IGS sub-repeats

Question 17

Gene conversion

Answer 17

(promoting greater or lesser diversity)
can result between genes that share a similar sequence, through the formation of a heteroduplex and the subsequent repair either converting the sequence of the invading strand or preserving it

Question 18

Transposition (aka jumping genes)

Answer 18

In the given example the cDNA inserts itself randomly via SINE (short interspersed elements)
Transposition is not covered in this presentation

Question 19

Shuffling genomes: the role of recombination

Answer 19

In sexual organisms, gametes are generated during the process of meiosis, and sometimes homologous chromatids overlap and exchange DNA. This is ‘recombination’.

This is important because evolution happens at the level of populations and is based on the combination of genes available

On a larger scale, chromosomes can mutate in ways that may changethe DNA content - e.g. resulting in the loss of DNA (deletion) orchanging the direction of the sequence (inversion), or simply involvethe moving of DNA among chromosomes (translocation).

Question 20

Structural changes over evolutionary time

Answer 20

*Synteny – physical co-localization of genes on chromosomes. Synteny maps are used to show genetic similarity of chromosomes between species e.g. snyteny maps shows closer genetic similarity between pigs and humans which both have high genetic complexity than between fish and humans

*Duplication – leads to paralogous genes

Whole genome duplication event led to modern fish species

Question 21

Pangenome

Answer 21

Chromosome structures are different from one human to another

research in this field is referred to as pangenome

Question 22

General conclusions

Answer 22

Nuclear genomes are in a constant state of flux, and composed of much sequence for which we still know little about possible functions. Much repetitive DNA may be generated as a by-product - errors generated when normal genomic processes related to DNA replication, transcription, repair and recombination go wrong. We take advantage of these regions to help us learn about genomic function and evolution

Question 23

Summary

Answer 23

1) A genome is the full complement of DNA carried by a single gamete –usually considered in terms of the organelle (i.e. nuclear, mitochondrial or chloroplast)

2) Genomes vary greatly in size among taxa – mostly due to differences in quantity of non-coding DNA

3) The proportion of genomic material represented by coding genes is small

4) Genes are structured and the rate of change over time (an interaction between mutation and selection) varies in coding and non-coding parts ofgenomes

5) Repetitive DNA is common and changes quickly over evolutionary time, by mechanisms distinct from point mutations (as seen in single copy sequences) and driven by errors made during the alignment and replication of repetitive regions.

6) Genomic flux by similar processes (translocations, inversions, crossing over, duplications) leads to poorer synteny among more distant genomes