Comparative Genomics I & II (Lectures 6&7)

Question 1

COMPARATIVE GENOMICS: – It’s All About
Similarities and Differences

In the genomes of contemporary related organisms, we see the conservation of: 2

Answer 1

In the genomes of contemporary related organisms, we see the conservation of:

1. • sequences coding for proteins and functional
     RNAs from a last common ancestor
2. • sequences controlling the regulation of genes
     that have similar patterns of expression

Question 2

Comparative Genomics : divergence? conservation? recognition?
= 4

Answer 2

1. Divergence is seen between sequences that code for proteins, functional RNAs and regulatory regions
   
   2. • responsible for differences between species
2. Conservation of sequence implies conservation of function
3. Recognition of orthologues and paralogues to make meaningful comparisons

Question 3

Comparative Genomics – It’s All About
Similarities and Differences AND the
Questions You Ask

Comparisons ACROSS LONG phylogenetic
distances, e.g. 1 billion years since separation: GIVES US? 2

Answer 3

Comparisons across long phylogenetic
distances, e.g. 1 billion years since separation:

1. *give information on types and numbers of genes in functional categories
2. *show little conservation of gene order and regulatory sequences

Question 4

Comparative Genomics – It’s All About
Similarities and Differences AND the
Questions You Ask:

Comparisons ACROSS MODERATE distances, e.g.70-100 million years since separation show: 3

Answer 4

Comparisons across moderate distances, e.g. 70-100 million years since separation show:

1. *functional and non-functional DNA is found in conserved regions
2. *functional sequences will have changed
   less than non-functional DNA
3. *purifying (aka negative) selection –
   removal of deleterious mutations

Question 5

UNDERSTAND PHYLOGENETIC TREES

Answer 5

DIAGRAM AND IMAGE ON SLIDE 4

Question 6

Comparative Genomics – It’s All About
Similarities and Differences AND the
Questions You Ask:

Comparisons ACROSS SHORT DISTANCES, e.g. 5 million years since separation give: 3

Answer 6

Comparisons across short distances, e.g. 5 million years since separation give:

1. *information about what sequences are
   responsible for making organisms unique
2. *differences due to positive selection (aka Darwinian selection)
3. *retention of mutations that benefit an
   organism

Question 7

Comparative Genomics – What is
Compared? = 19

Answer 7

1. Repeat regions
   
   2. *transposable elements, microsatellites
2. Markers
   
   4. *SNPs
3. Non-protein coding regions
   
   6. *RNA-only genes
   7. *gene deserts
4. Duplications
   
   9. *whole genome
   10. *segmental
   11. *gene
   12. *gene families
5. Base composition, e.g. %GC content
   
   14. *overall
   15. *coding regions and non-coding regions
6. Gene number in functional categories
7. Favourite genes
8. Chromosome rearrangements
9. Gene order

Question 8

Synteny?

Answer 8

*genes or genetic elements located
on the same chromosome

*may or may not be linked

Question 9

Conserved (aka Shared) synteny?

Answer 9

*conservation of synteny of
orthologous genes between two or
more different organisms

*extent is inversely proportional to
length of time since divergence
from the ancestral locus

Question 10

Collinearity?

Answer 10

Collinearity
*conservation of gene (or marker) order along a chromosomal segment in different
species

*Note: in much present-day usage, synteny has same meaning as collinearity

Question 11

Collinearity diagram

Answer 11

A-E = genes or markers; X-Z = species; coloured boxes = coding regions slide 8

Question 12

Synteny, Conserved Synteny and Collinearity: SIGNIFICANCE? = 2

Answer 12

1. *in genomes of some grasses see high conservation of synteny and collinearity
   
   2. *knowing the genome sequence of a species with a small genome facilitates mapping and isolating genes coding for desirable traits from species with larger genomes
2. *in medicine
   
   4. *loci with medical or phenotypic consequences can be recognised because of linkage to a cluster of syntenic loci

Question 13

Factors affecting synteny, conserved synteny and collinearity?

Answer 13

*gene loss, multiple rounds of gene
duplications, chromosomal
rearrangements (fusions, splits,
inversions, reciprocal translocations)

*mask sequences that have been
derived from a common ancestral
sequence

Question 14

Synteny, Conserved Synteny and Collinearity DIAGRAM

Answer 14

SLIDE 9

Question 15

Evolutionary Convergence: WHAT IS PHENOTYPIC CONVERGENCE?

Answer 15

1. *the independent evolution of similar or identical traits
   in distantly related species due to selective
   pressures, for example:
2. *eyes
3. *echolocation in dolphins and bats
4. *particular protein properties
5. *biochemical pathways

Question 16

Evolutionary Convergence: WHAT DOES PHENOTYPIC CONVERGENCE DO? 3

Answer 16

1.IDENTIFY THE DETERMINANTS leading to the independent origins of adaptive traits

2. *COMPARING DETERMINANTS gives INFORMATION on the GENOMIC (and ENVIROMENTAL) background in LIMITING OT FURTHERING ADAPTATIVE INFORMATION
3. *“evolutionary enablers”

Question 17

Evolutionary Significance of Convergent Recruitment….5

Answer 17

1. The presence of genes able to evolve a new function enhances the chances that a given group of organisms can evolve a new trait
   2. *but only a few genes have the potential to make a specific phenotypic change
2. *“evolutionary enablers”
3. AND….
4. The absence of these genes (evolutionary enablers) in other groups of organisms can hinder the acquisition of a new trait

Question 18

Evolutionary Significance of Convergent Recruitment…DIAGRAMS

Answer 18

WITH AND WITHOUT EVOLUTIONARY ENABLERS…

SLIDE 11 AND 12

Question 19

Evolutionary Convergence – How Does It Happen?

• Phenotypic convergence may result from:

Answer 19

1. *alterations of different loci shows changes —> in different enzymes can lead to similar phenotypes
2. *alteration of homologous genes from different Taxonomic groups —> CONVERGENT RECRUITMENT

Question 20

Evolutionary Convergence – How Does It Happen?

New functions usually evolve by the modification of pre-existing genes
*two criteria need to be met:

Answer 20

New functions usually evolve by the modification of pre-existing genes
*two criteria need to be met:

1) no deleterious effect through loss of ancestral function

2) expression profiles of the genes and kinetics of the proteins they encode must be suitable for new function

Question 21

Evolutionary Convergence – How Does It Happen? KREBS CYCLE DIAGRAM

Answer 21

At least 60 independent origins of the
C4 photosynthetic pathway have
occurred in the flowering plants – an
excellent example of convergent
evolution

SLIDE 13

Question 22

Convergent Recruitment – e.g. PEPC Genes in C4 Monocot Lineages:

‘Evolution of phosphoenolpyruvate carboxylase (PEPC) gene in groups
of grasses (g) and sedges (s)’ = 4

Answer 22

1. *PEPC = enzyme catalysing first reaction of C4 photosynthesis
2. *letters and numbers after g and s = PEPC gene lineages
3. *red and blue triangles = PEPC gene lineages important in C4
   grasses and sedges

DIAGRAM IN SLIDE 14

Question 23

Convergent Recruitment – e.g. PEPC Genes in C4 Monocot Lineages

‘Evolution of phosphoenolpyruvate carboxylase (PEPC) gene in groups
of grasses (g) and sedges (s)’ FOUND? = 3

Answer 23

1. *grasses – same lineage of PEPC gene (out of 6 lineages) used
   > 8 times during the evolution of C4 grasses
2. *sedges – same lineage of PEPC gene (out of 5 lineages and distinct from that used by grasses) used > 5 times during
   evolution of C4 sedges

—–>

3. The predisposition of these gene lineages to evolve novel adaptive
   function

Question 24

Convergent Recruitment – e.g. PEPC Genes in C4 Monocot Lineages

‘When there is phenotypic convergence due to convergent recruitment:’ 7

Answer 24

1. When there is phenotypic convergence due to convergent recruitment:
   2. *may see identical substitutions in the recruited
      genes in different lineages of organisms
      
      3. *e.g. C4 PEPC genes in grasses (b) and sedges (c) Note: protein sequences shown
      4. *likely to occur because effects of the resulting amino acid substitutions will be comparable
      5. *limitations to substitutions that can occur
      6. *allow emergence of functional, optimised protein
2. Note: convergent substitutions do not explain all the convergent phenotypes seen – non-convergent (= divergent) substitutions also play a role in these adaptive changes

Question 25

Convergent Recruitment – e.g. PEPC Genes in C4 Monocot Lineages IMPORTANAT SLIDE DIAGRAM

Answer 25

SLIDE 15

Question 26

Comparative Genomics of Prokaryotes = 5

Answer 26

1. Smaller genomes found in organisms living in restricted environments – e.g. ‘Nanoarchaeum equitans’ lives inside another archea
2. Larger genomes in organisms living in complex habitats – e.g. ‘Bradyrhizobium japonicum’, soil bacterium that forms symbiotic relationship with plants (nitrogen-fixing root nodules)
3. Why….?
4. Constant environments may allow
   survival with fewer genes
5. Changeable habitats e.g. soils –
   many genes would be required for
   survival even though they all may not
   be used all the time

Question 27

Comparative Genomics of Prokaryotes – e.g. Influence of HGT and IGD on Protein Family Expansion : 5

Answer 27

1. Prokaryotes show rapid adaptation
   
   2. *in part due to the acquisition of genes by horizontal gene transfer (HGT)
   3. *increases genome size
   4. *in part due to intrachromosomal gene duplication (IGD)
      5. *increases genome size

Question 28

Comparative Genomics of Prokaryotes – e.g. Influence of HGT and IGD on Protein Family Expansion DIAGRAM

Answer 28

SLIDE 18

Question 29

Comparative Genomics of Prokaryotes –

e.g. Influenceof HGT and IGD on Protein Family Expansion

Answer 29

110 genomes representing eight distinct clades of prokaryotes compared

*different genome sizes – small (blue), average (red), large (purple)

Question 30

Comparative Genomics of Prokaryotes –

e.g. Influence of HGT and IGD on Protein Family Expansion

‘SEARCHED FOR:’ 2

Answer 30

1. *paralogues – homologues acquired through IGD – identical in sequence to endogenous gene and tandemly arranged
2. *xenologues – homologues acquired through HGT – randomly arranged and showing sequence variability to the endogenous gene

Question 31

Comparative Genomics of Prokaryotes –

e.g. Influence of HGT and IGD on Protein Family Expansion

FOUND: 5

Answer 31

1. Found: 88% - 98% of expansions due to HGT
   
   2. *both small and large genomes
   3. *larger genomes contained the most xenologues
      (contrary to previous thinking)
2. paralogues have higher expression levels than xenologues
3. xenologues had higher expression levels than singletons

Question 32

WHO ARE NEANDERTHALS? = 3

Answer 32

1. Neanderthals and the ancestors of modern humans diverged
   270,000 to 400,000 years ago
2. *Neanderthals = sister group to modern humans
3. Neanderthals and modern humans
   coexisted in Europe for 30,000-45,000 years ago

Question 33

Why sequence the Neanderthal genome?
= 2

Answer 33

1. *record changes (mutations) that have become fixed or risen to high frequency in humans in the last several hundred thousand years
2. *identify genes that have been affected by positive selection since Neanderthals and humans diverged

Question 34

UNDERSTANDING Neanderthal and Modern Human Genomes ..STUDY

What DNA is used? from where? = 9

Answer 34

1. Majority of DNA used in the 2010 study was extracted from
   2 *bones of three females
   3 *Vindija cave (Croatia)
2. Other samples from bones of Neanderthals in
   5 *Spain
   6 *Germany
   7 *Russia
3. More recently other ancient
   human genomes have been
   sequenced
4. Many more comparative analyses
   followed

Question 35

Neanderthal and Modern Human Genomes INVESTIGATION PROCESS:

CONTROLS? USED? ASSEMBLED? COMPARED WITH? = 15

Answer 35

1. Ran numerous controls and checks to exclude contamination
   2 *microbial DNA
   3 *modern human DNA
2. Used NGS technologies
3. Assembled sequence using reference genomes
4. *chimpanzee
5. *modern human genome (Ventner)
6. Compared sequence with
7. *chimp
8. *Ventner
9. *South African (San)
10. *West African (Yoruba)
11. *Papua New Guinean
12. *Chinese (Han)
13. *Western European (Frenc

Question 36

Neanderthal and Modern Human Genomes …WHAT HAPPENED TO THE GENOME? = 8

Answer 36

1. One-third of genome not sequenced
2. *DNA not of high enough quantity and/or quality
3. Genomes are 99.84% identical
   
   4. *78 nucleotide substitutions in protein-coding genes in 300,000 years
      
      5. *modern humans have derived state of these genes
      6. *Neanderthals have ancestral (chimp-like) state
   5. *genes include those coding for proteins involved in skin physiology
      8. * not clear what effect these changes have at the phenotype level

Question 37

Neanderthal and Modern Human Genomes …COMPARED SNPs between Neanderthals and present-day humans…= 7

Answer 37

1. Compared SNPs between Neanderthals and
   
   2. *present-day humans
      
      3. *2 European Americans
      4. *2 East Asians
      5. *4 West Africans
2. *diverse modern humans (French, Yoruba, Han, San, Papuan)
3. *chimps

Question 38

Neanderthal and Modern Human Genomes:

Compare SNPs between Neanderthals and present-day humans…FINDINGS = 3

Answer 38

1. Neanderthals share more SNPs with
   Europeans and East Asians than sub-Saharan Africans, suggesting….

       2. gene flow from Neanderthals to modern humans after modern humans left Africa, but before migrating into Eurasia

2. 1-4% of modern Eurasian genomes derived from Neanderthal genomes

Question 39

Comparisons of Neanderthal and modern
human Y chromosome (father to son
inheritance)

and mitochondrial DNA (mtDNA;
mother to all progeny)

FINDINGS = 6

Answer 39

1. Different evolutionary history for Y
   chromosome and mtDNA compared to
   autosomal genomes
2. 360,000 to 200,000 years ago
   
   3. • complete replacement of Neanderthal mtDNA and Y chromosome with those of modern humans
   4. • low percentage of X and autosomal genes transferred
3. 80,000 to 40,000 years ago
   
   6. • Neanderthal X chromosome and autosomal gene flow to modern humans

Question 40

Neanderthal and Modern Human Genomes :
?? Why replacement ??

FOR THE Y CHRO. = 5

Answer 40

For the Y chromosome:

1. Neanderthal population size = lower than H. sapiens population when the two species were separated (700,000 to 500,000 years ago)
   ===>
2. Accumulation of deleterious genetic variants

====>
3. Lower fitness

4. Simulations of deleterious variant accumulation suggest:
   …5. * 1-2% Y chromosome fitness reduction increases replacement probability after 50,000 years to 25-50%

Question 41

Neanderthal and Modern Human Genomes: NEANDERTHAL DNA…COVID-19 AND HIV …. = 11…50KB REGION

Answer 41

1. Neanderthal DNA
   * 50 kb region
   
   2. • presence on chromosome 3 raises risk of severe COVID-19
      3. • haplotype = frequency of 30% in individuals of south Asian ancestry
      4. • rare in east Asian and African populations; 4% Latin Americans, 8% Europeans
2. • hypothesised to be important in the immune response to other pathogens but elicits hyper response with COVID-19 infection*
3. • region encodes a cluster of chemokine receptors
     
     7. • includes coreceptor for HIV
          8. * downregulated in carriers of COVID-19-risk haplotype
          
          • ~27% lower risk of HIV infection
4. Risk factor predates HIV pandemic
5. • HIV not the selection driver
6. • smallpox virus, Vibrio cholerae (cholera)?
7. • highest frequency found in regions where cholera is endemic

11.*genetics only one factor in developing severe COVID-19

Question 42

Neanderthal and Modern Human Genomes: NEANDERTHAL DNA…COVID-19 AND HIV …. = 7…75KB REGION

Answer 42

1. Neanderthal DNA
   * 75 kb region
2. • presence on chromosome 12 protects against severe COVID-19
     3. * haplotype = frequency of ~25-30% in most Eurasian populations
     4. * rare in African populations south of the Sahara; at lower frequency in some
     populations in the Americas (African or Native American ancestry)
3. • several genes encode enzymes (oligoadenylate synthetases; OAS) induced by interferons and ds-RNA
     6. * downstream pathways that lead to degradation of intracellular ds-RNA and activation of antiviral mechanisms
     7. * at least one (OAS1) shows positive selection

Question 43

Grass Genomes – WHAT IS IT? Why Study Them Using Comparative Genomics? = 6

Answer 43

1. Grasses (Cereals)
2. *provide the bulk of human nutrition
3. *feed for animals
4. *sustainable energy sources – biofuels
5. BUT consumption is close to supply; stocks have plateaued
6. Comparative genomics gives insights into resistance to biotic and abiotic stresses; growth; production; yield; other desirable traits

Question 44

UNDERSTANDING Grass Genomes:
= 8

Answer 44

1. Three subfamilies contain major food, fodder and fuel grass species
2. *ancestor of all underwent whole genome duplication (WGD; shown)
   3. *lineage-specific WGDs also occurred (not shown)
3. Whole-genome sequence available for at least one species in each subfamily
4. ‘Brachypodium distachyon’ (Brachy)
5. representative of subfamily containing barley and wheat
   7.relatively small genome for this subfamily
   
   8. *1/10 the size of barley and wheat

Question 45

Brachy Genome Compared to Other Grass
Genomes – Transposable Elements = 8

Answer 45

Brachy
1. *genome size and gene number – similar to rice and sorghum
2. *maize is larger due to lineage-specific WGD

3. *chromosome number – half that of others
4. most LTR retrotransposons located in
   pericentromeric regions and conserved syntenic breaks
   5.also seen in other grass genomes
5. *DNA transposons more widely distributed
6. *majority associated with gene rich regions
7. *also seen in other grass genomes

Question 46

DIAGRAM: Brachy Genome Compared to Other Grass
Genomes – Transposable Elements

Answer 46

SLIDE 33

LTR = long terminal repeat; STA = gene introns and satellite
tandem arrays; cLTRs = complete LTRs; sLTRs solo LTRs; DNATEs = autonomous DNA transposons; MITES = miniature
inverted-repeat transposable elements; CDS = gene exons;
triangles = syntenic breakpoints

Question 47

Brachy Genome Compared to Other Grass
Genomes – Transposable Elements

‘From comparative analyses on sequenced grass genomes can conclude:’ = 2

Answer 47

1. retrotransposon content scales with genome
   size for all grass genomes
2. • DNA transposon content is not correlated with
     genome size for all grass genomes

Question 48

Brachy Genome Compared to Other Grass
Genomes - Conservation of Gene Families = 7

Answer 48

1. 77% - 84% of gene families found in rice, sorghum and Brachy are shared
   
   2. *reflects relatively recent common origin
2. Lineage-specific genes
3. *genes for which no orthologue can be found in related species
4. *taxonomic levels = grass, grass subfamily (Pooid), Brachy
5. *obvious targets for functional analyses
6. *may be involved in distinguishing taxa

Question 49

Brachy Genome Compared to Other Grass
Genomes - Conservation of Synteny

‘In Brachy: six major duplications of chromosomal regions’ = 4

Answer 49

1. In Brachy: six major duplications of chromosomal regions
2. *covering 92% of the genome
3. *originated from the ancient WGD event before grass families diverged
4. *creation of paralogues

Question 50

Brachy Genome Compared to Other Grass
Genomes - Conservation of Synteny:

‘Conserved synteny between Brachy, rice,
sorghum and wheat’ = 5

Answer 50

1. Conserved synteny between Brachy, rice, sorghum and wheat
   2. *59 blocks of collinear orthologous
      genes
2. *covering 99% of the Brachy genome
3. *provide a framework for
   understanding grass genome evolution
4. *aid the assembly of sequences from
   other related grasses

Question 51

brachy Genome Compared to Other Grass
Genomes - Conservation of Gene Families Diagram

Answer 51

slide 35

Question 52

Brachy Genome Compared to Other Grass
Genomes - Conservation of Synteny diagram

Answer 52

slide 36