S1: W4 (Prof. Kelsey) Flashcards by Palesa Mamabolo

Knowing the three acts of a genome: What are the three acts?

● Act 1
= Who?

● Act 2
= What?

● Act 3
= Why?

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Act 1?

= what exactly is a genome? & what can it tell us?

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Genome?

= complete genetic materials in a DNA molecule of an organism.

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Components of a genome generally? (5)

• Protein-coding genes
• Non-coding genes.
• Junk DNA.
• Mitochondria & mt genome (eukaryotes).
• Chloroplasts & cp genome (algae & plants).

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Eukaryotic genome components? (2)

• Repetitive DNA sequences.
• Non-repetitive DNA sequences.

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Eukaryotic genomes attributes? (4)

• Single copy in haploid genome.
• Repetitive sequences are present in >1 copy.
• Larger genomes don’t have more genes, but more junk/repetitive DNA.
• Non-repetitive sequences are unique.

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Junk DNA?

= a DNA sequence that has no relevant biological function.

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Why is it called Junk DNA?

It’s because scientists haven’t designated a specific function to it.

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Types of repetitive DNA? (2)

• Satellite DNA.
• Interspersed repeats.

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Relate level of complexity of organism to DNA?

More complex organism, more repetitiveness.

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Endosymbiosis attributes? (3)

• Responsible for mt & cpDNA.
• Most of the genes of the mt & cp genomes have been transferred to the nucleus, driving the organelle’s evolution.

• Bacterium evolves into mt, losing genes that are necessary for its development.

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Why do we have mitochondria? (3)

• Help build the organelle’s internal structure.
• Allow localized bioenergetic modulation.
• Less sensitive to hybridization.

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Why map a genome? (3)

• Individual genomes show extensive variation.
• Where is it? How did it get there?
• Polymorphism found at the phenotype level when a sequence affects the gene functions.

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Genome mapping types? (2)

• Linkage maps.
• Restriction maps.

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Genome mapping attributes? (2)

• Uses linkage maps.
• Uses restriction maps.

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What are linkage maps based on?

Frequency of recombination between genetic markers.

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What are restriction maps based on?

Physical distances between the markers.

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How are genomes mapped?

By sequencing their DNA & identifying functional genes.

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GWS attributes? (3)

• Associate a specific trait with a genotype (SNP).
• Identify SNPs that are more frequently found in patients with a particular disorder.
• SNPs can be associated with genetic disorders/other traits of interest.

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Genome sequencing & Evolution attributes? (2)

• Differs in the level of complexity/requirements of an organism that enable it to function well.
• No. of genes in bacterial & archaeal genome is proportional to genome size.

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How many different types of genes are there?

Many genes are duplicated & the no. of different gene families is much smaller than the total no. of genes.

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Human genome attributes? (4)

• Fewer genes than originally expected.
• Genomes occupy 25% of human genome, but protein-coding sequence are only a small part of fraction.
• Exons comprise ~5% of each gene, so genes (exons & introns) are ~25% of the genome.
• Human genome has ~20 000 genes.

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How many genes are essential for life?

We don’t fully understand the persistence of genes that might be unused in the genome as a systematic analysis of loss of function for 86% of worm genomes shows that only 10% have detectable effects on the phenotype.

Genomes & Evolutionary questions? (2)

• Is organismal diversity due to presence/absence of certain genes?

• Why do mammals, amphibians & plants have larger genomes?

Is organismal diversity due to presence/absence of certain genes? (2)

• Many gene families are expanded by duplication. • Coincides somewhat with diversification of Metazoa.

Eg of Evolutionary Q1?

Teleost fish.

Act 2?

= What? & speaks on how genomes come in all sizes.

Genome size attributes? (4)

• Varies a lot. • Specialized in function. • Genome size is associated with organisms of high complexity & tighter regulations for cell function. • Bigger isn't always better.

Larger genomes results/effects? (3)

• High chances of aberrations in organisms/more suffering. • Difficult maintenance. • Slower development. *All effects due to high energetic requirements.

Why aren't bigger genomes always better?

Explain effects of having larger genomes.

Eg of Specialized in function in Genome size?

GP vs Specialists.

Eg of Why bigger/more genomes aren't always better?

Article of how extra DNA had deformed the bodies, hearts & brains of salamanders.

Act 3?

= the Why & How of genomes.

Gene duplication attributes? (4)

• Contributes to genome evolution. • Slow process. • Results in gene families. • Pseudogenes lose their original function.

What causes pseudogenes to lose their original function? (2)

• Reverse transcription. • Integration of mRNA transcripts.

Cause of non-processed Pseudogenes?

Incomplete duplication.

Selfish genes?

= genes whose only goal is to replicate & be inherited.

Selfish genes attributes? (2)

• Function is unknown yet. • Contribute to large parts of junk DNA.

Molecular phylogenetic tree?

= tree showing relationship between lineages.

Molecular phylogenetic tree attributes? (4)

• Can be produced using molecular data. • Based on molecular data. • General term. • Lineages might be computed from genome-wide DNA or a single gene.

Gene tree?

= phylogenetic tree computed from data coming from a single gene.

Egs of Gene trees? (2)

• COI based tree (plastid marker). • ITS based tree.

Species tree?

= phylogenetic tree computed from genome-wide DNA data.

Species tree attributes? (2)

• An amalgamation of gene trees. • Based on multiple markers or the entire gene.

Egs of Species trees? (2)

• Multi-locus tree. • NGS tree.

Gene tree vs Species tree? (2)

● Amount of data used. ● Origin of data used.

Is a gene tree not just a species tree with fewer data?

No.

Reasons why gene trees & species trees are incongruent? (4)

● Genes can have unequal rate of evolution (divergence often precedes speciation). ● Gene loss & gene duplication are common. ● Gene flow can occur between lineages after their separation. ● Recombination between neighbouring gene regions.

Eg of Reason 1?

Hypoxis parvula var. albiflora & Hypoxis parvula var. parvula.

Explain Eg of Reason 1? (2)

• Even though they look different they are related. • Gene tree shows they're different but species tree shows that they're of the same species.

Terms to recall for Reason 2? (3)

• Homolog. • Ortholog. • Paralog.

Eg of Reason 3?

Rhodohypoxis baurii & Hypoxis parvula.

Explain Eg of Reason 3? (2)

• Mate regardless of morphological differences & being different species/unrelatedness. • Gene tree fails to separate species in the occurrence of gene flow but species tree is able to do so successfully.

Why care about gene trees at all in phylogenetics/gene trees importances? (5)

• Building blocks of species trees. • To determine the evolutionary history of a gene family. • Infer gene duplications & losses. • Estimate bounds of times these events occurred. • Determine if a given pair of homologs are orthologs or paralogs.

What do you mean by "estimate bounds of times these events occurred"?

We mean to estimate the speed at which these events occurred & track them.