Genomes and Their Evolution

Question 1

What is genomics?

Answer 1

• The study of genomes
• Involves analysis of whole sets of genes and their interactions

Question 2

What is transcriptomics and proteomics?

Answer 2

The study of entire sets of RNA molecules and proteins

Question 3

General properties of genomes

Answer 3

• Genome size, number and gene density vary within and between eukaryotes and prokaryotes
• Alternate splicing increases protein diversity without increasing genes
• Non-coding DNA is not necessarily non-functional

Question 4

What is high-throughout sequencing?

Answer 4

Generate enormous amounts of data very rapidly

Question 5

Illumina Advantages

Answer 5

• High accuracy
• Low error rate

Question 6

Illumina Disadvantages

Answer 6

Short read length makes genome assembly difficult

Question 7

Pacific Biosciences and Nanopore Advantages

Answer 7

Long read length improves genome assembly

Question 7

Pacific Biosciences and Nanopore Disadvantages

Answer 7

• Lower accuracy
• Higher error rate

Question 8

What is a microbiome?

Answer 8

The collective genomes of all microorganisms living in an environment

Question 9

What its metagenomics?

Answer 9

• Study of the microbiome using high-throughout sequencing

Question 10

What is ancient DNA?

Answer 10

• DNA isolated from ancient samples
• Can be sequenced

Question 11

What is bioinformatics?

Answer 11

The use of computer software to analyze sequencing data

Question 12

What is gene annotation?

Answer 12

Prediction of genes in genome sequencing and the function of the gene products

Question 13

What is systems biology?

Answer 13

• It aims to understand whole cellular systems
• Goal of being able to predict biology

Question 14

What are genome-wide association studies?

Answer 14

• A method to associate genetic variation across a population with specific phenotypes
• Can be used to identify genomic regions associated with disease risk or other traits

Question 15

What accounts for 1.5% of the human genome?

Answer 15

• DNA sequences (exons) coding for protein, rRNA or tRNA

Question 16

What accounts for 25% of the human genome?

Answer 16

• Gene-related DNA, including introns and regulatory elements

Question 17

What accounts for the rest of DNA?

Answer 17

• non-coding DNA
• Repetitive elements
• Unique sequences

Question 18

What are transposable elements?

Answer 18

• A segment of DNA that can move around and within the genome of a cell
• 20-50% of mammalian genomes

Question 19

What is a transposon?

Answer 19

• Moves via a DNA intermediate
• Copy-and-paste mechanism of movement

Question 20

What is a retrotransposon?

Answer 20

• Moves via a RNA intermediate
• Copy-and-paste mechanism
• In eukaryotes, retrotransposons are more common than transposons

Question 21

Alu Elements

Answer 21

• About 300 nucleotides long
• account for 10% of the genome
• Help regulate gene expression

Question 22

LINE-1 retrotransposons

Answer 22

• About 6500 base pairs long
• About 17% of the genome
• Contribute to neuron development

Question 23

Transposable elements and evolution

Answer 23

• Can facilitate chromosomal translocations by providing sites for unequal homologous recombination leading to gene movement
• Disrupt genes, or modify rates of transcription
• Most changes are harmful, sometimes provide a benefit

Question 24

Why is there repetitive DNA?

Answer 24

Due to errors in DNA replication or recombination

Question 25

What are large-segment duplications?

Answer 25

Scattered copies of long sequences, copied from one region of the genome to another

Question 26

What is simple sequence DNA?

Answer 26

- Tandemly repeated sequences - Each repeat is 2 to 500 nucleotides long - Found at telomeres and centromeres

Question 27

What is a short tandem repeat?

Answer 27

- Simple sequence DNA with each repeat being 2 to 5 nucleotides long

Question 28

Genome rearrangement affect?

Answer 28

Usually harmful but may provide benefit

Question 29

What do translocations and fusions cause?

Answer 29

- Alterations in chromosome structure - Contributes to the emergence of new species

Question 30

What does polyploidy mean?

Answer 30

- When there are 3 copies of chromosomes - Normally lethal but not always - More common in plants, can lead to a new species

Question 30

What causes polyploidy?

Answer 30

Duplication of entire chromosome sets via nondisjunction

Question 31

How can polyploidy lead to a new species?

Answer 31

One set of genes provides essential functions while the other set(s) diverges through mutation

Question 32

What happens when there is unequal crossing over during meiosis?

Answer 32

- Lead to duplication and deletion of chromosomal regions

Question 33

What happens if DNA polymerase slips during DNA replication?

Answer 33

- Small duplications or deletions - Contributes to changes in repeat numbers in short tandem repeats

Question 34

What are multigenerational families?

Answer 34

- Collections of two or more similar genes with a common origin - Usually clustered and often have RNAs as their final product

Question 35

Evolution of the global multigenerational families

Answer 35

- Includes the alpha-globin and beta-globin gene families originating from a single ancestral gene

Question 36

How were the global multigene families formed?

Answer 36

By duplications followed by a mutation leading to functional diversification

Question 37

Evolution of genes with new functions

Answer 37

- Lysozyme breaks bacterial cell walls - alpha-lactalbumin regulates milk production in mammals - Alpha-lactalbumin evolved from a duplicated lysozyme gene with mutations