Gene Duplication

Question 1

What happens when one progresses from a more basal organism to derived ones?

Answer 1

There’s a general increase in genome size and gene number as one progresses from them.

Question 2

Retrotranspisition of the mRNA of a gene leads to…?

Answer 2

Retrotransposition of the mRNA of the gene leads to the random integration of an intron-less paralogue at a distinct genomic location

Question 3

– TRUE OR FALSE -
Gene duplication rate is 10,000x greater than the base substitution rate (~10**9/site/generation)

Answer 3

TRUE

Question 4

What do Gene family or Multigene family consist of?

Answer 4

They consist of orthologous and paralogous genes which are derived from a common ancestral gene.

• Generally maintaining similar biochemical function
• Members of a gene family are generally clustered together on the same chromosome, but they can be dispersed on different chromosomes or a combination.

Question 5

How is gene family characterized?

Answer 5

• Sequence similarity at the amino acid level
• Auxiliary evidence, such as functional similarity or tissue-specificity (this allows for improved classification)
• Gene family size = number of genes within a gene family
• Gene family size can vary considerably

Question 6

What is the term superfamilies?

Answer 6

It was introduced to delineate between closely and distantly related proteins

Question 7

Give an example of a superfamily

Answer 7

Globin Superfamiily

Question 8

What are gene families?

Answer 8

Gene families are groups of genes that share similar sequences and functions, typically derived from a common ancestor through gene duplication and divergence over evolutionary time. These families are essential for understanding the organization and evolution of genomes and the diversity of biological functions encoded within them.

Question 9

Describe the possible fates of a duplicated gene

Answer 9

Duplicated genes can undergo subfunctionalization (partitioning of ancestral function), neofunctionalization (acquisition of new function), or pseudogenization (loss of function).

The most common fate is that one member of the pair is deleted to return the gene to the singleton state.

Other paths involve the reduced expression of both copies (hypofunctionalization) that are held in duplicate to maintain sufficient quantity of function.

Question 10

Describe genome duplication (polyploidization)

Answer 10

Genome Duplication is also referred as whole-genome duplication (WGD) or polyploidization and its caracterized by a cell or organism having a genome with multiple (more than 2) sets of homologous chromosomes.

Haploid (N)
Diploid (2N)
Triploid (3N)
Tetraploid (4N)
Hexaploid (6N)

Question 11

In which species we can expect to see Polyploidy?

Answer 11

Polyploids are common among plants, as well as among certain groups of fish and amphibians.

Norm in ferns - 95% of all species

Question 12

What are the consequences of Polyploidy?

Answer 12

• Phenotypic level*
• effects are often mild and idiosyncratic
• Cell volume and size*
• cell volume generally increases with in creasing genome size

Genome instability
-polyploid genomes are often unstable and undergo repatterining and segmental loss

Question 13

Explain Diploidization

Answer 13

Is the evolutionary process whereby a tetraploid species “decays” to become a diploid with twice as many distinct chromosomes.

(four alleles a a locus to two alleles at each of two distinct loci)

Question 14

A nucleic acid sequence in DNA that can change its position (transpose) within a genome, sometimes creating or reversing mutations and altering the cell genetics identity (jumping genes)

Answer 14

Transposable Elements

Question 15

Selfish genetic elements

Answer 15

Transposable elements

Question 16

Two major classes of Transponsable Elements:

Answer 16

Copy-and-Paste
- retrotansposons
- Duplicative/replicative transposition
- TE makes a copy of itself and moves to a new location
- it undergoes reverse transcription
Cut-and-Paste
- DNA transposon
- DNA intermediate
- Non-replicative/Conservative transposition
- TE does not make a copy of itself when it moves to a new location.

Question 17

What’s the evolutionary impact of TEs:

Answer 17

1. Genome size
2. Mutations and genetic polymorphisms
3. Source of new regulatory elements affecting gene expression
4. Promote genomic rearrangements

Genome size
Genome size and TE content are correlated with each other. TE proliferation leads to an increase in genome size.

• Mutations and genetic polymorphisms*
  Most dramatic impact of TEs occurs when they insert into active genes.

Source of new regulatory elements affecting gene expression
TEs can also have an impact when they insert into noncoding regions near genes.
This can alter gene expression patterns, which can lead to dysregulation of gene expression, more likely deleterious.

Promote genomic rearrangements
this can lead to DNA replication errors

Question 18

What is heteroplasmy?

Answer 18

Heteroplasmy refers to the presence of more than one type of mitochondrial DNA within an individual.

Question 19

Why are organelle genomes smaller than bacterial genomes?

Answer 19

Organelle genomes (like mitochondria or chloroplast genomes) have undergone significant reduction in size due to gene transfer to the nuclear genome and loss of nonessential genes.
They often encode only a subset of genes necessary for organelle function, with many functions now carried out by nuclear-encoded proteins.
Some genes are absorbed by the host - selfish

Question 20

Function of mitochondria

Answer 20

Are the energy factories of eukaryotic cells

Question 21

Where did all the genomic material and associated genes of organelles go?

Answer 21

Diminished size following endosymbiosis due to:
- loss of genetic material
- transfer of genetic material to the nuclear genome

Transfer of organellar genes to the nucleus

Question 22

Transfer of nonfunctional DNA segments from organelles to the nucleus:

Answer 22

Numts and Nupts

Numts : nuclear mitochondrial
Nupts : nuclear plastid DNA sequences

Question 23

Causes for elevated mitochondrial rates of evolution in animals?

Answer 23

1. Low fidelity of the DNA replication process in animal mitochondria
2. Inefficient repair mechanism
3. High concentration of mutagens (e.g. superoxide radicals) resulting from the metabolic functions by mitochondria
4. Effective population sice that is 1/4 that for nuclear genes