Genomes

Question 1

What are the two main ways to determine genome size?

Answer 1

Estimate of nuclear particle size
Direct sequencing

Question 2

What is the process of Feulgen staining in assessing genome size?

Answer 2

HCL followed by Schiff reagent and ethanol wash
DNA should turn red
Intensity of reaction following hydrolysis of DNA is measured by a microdensitometer

Question 3

What is the process of flow cytometry in assessing genome size?

Answer 3

Laser detection of particle size in suspension

Question 4

What are smaller genomes associated with?

Answer 4

Forms tighter host associations

Question 5

What are larger genomes associated with?

Answer 5

Mobile DNA content

Question 6

What are the characteristics of microsporidia?

Answer 6

Unicellular parasites
Lack motile structures
Endospore contains chitin
Mitochondria are replaced by mitosomes

Question 7

What are mitosomes?

Answer 7

Lacks a genome and function is unclear
Has some of the proteins found in mitochondria

Question 8

What is the polar filament of microsporidia?

Answer 8

Harpoon mechanism
It is coiled and ready to deploy to infect cells, the tube transports contents to infected cell

Question 9

What are the two ways that microsporidia can develop in humans?

Answer 9

Proliferation within cytosol or proliferation within parasitophorous vacuoles

Question 10

How are DNA sequences determined using first-generation technology (Sanger sequencing)

Answer 10

Infer nucleotide identity using dNTPs then visualize with electrophoresis
Short-sequence reading

Question 11

How are DNA sequences determined using second-generation technology?

Answer 11

High throughput from the parallelization of sequencing reactions
Short-sequence reading

Question 12

How are DNA sequences determined using third-generation technology?

Answer 12

Sequence native DNA in real-time with single-molecule resolution
Long-sequence reading

Question 13

What are transposable elements?

Answer 13

DNA sequences that can move in the genome, can represent up to 85% of the genomic content

Question 14

What are class I (retrotransposans) TEs?

Answer 14

Copy and paste

Question 15

What are class II TEs?

Answer 15

Cut and paste

Question 16

What is the effect of TEs on fungal genomes?

Answer 16

Mobile elements have a neutral to negative effect by moving around DNA on the genome
Some rearrangements may generate mutational diversity that is beneficial
In asexual species, the mutational effects may offset the loss of allele shuffling

Question 17

What do genomic rearrangements sometimes produce?

Answer 17

Regions of concentrated repeats (islands) that can be rich in effectors, secretory and transmembrane proteins important in virulence
Sometimes they regions persist across meiosis as accessory chromosomes

Question 18

What are the functions of Spok protein?

Answer 18

It performs both killing and resistance functions

Question 19

How do Spok genes violate Mendelian laws?

Answer 19

It violates the law of segregation by killing the carrier of the other half of heterozygote alleles directly after meiosis, this kind of intragenomic conflict and favoring of one chromosome set over another is referred to as meiotic drive

Question 20

What are Spok blocks?

Answer 20

Collected Spok elements that can move around and can be present in at least 4 different genomic locations

Question 21

Why the varying positions of Spok blocks?

Answer 21

The Spok block is not only capable of meiotic drive but it is also capable of transposition

Question 22

What is the Enterprise?

Answer 22

One Spok block that is contained in a giant tyrosine-recombinase mobilized DNA transposon

Question 23

What does Kirc contain?

Answer 23

A domain called DUF3435 which is found to overlap in motif with tyrosine recombinases

Question 24

How can TEs with a spore-killing-related crypton (Kirc) occur?

Answer 24

With or without Spok block as cargo

Question 25

What is Kirc associated with?

Answer 25

Duplicated genes in ascomycetes

Question 26

What happens with the Spoks are captured by the Enterprise?

Answer 26

Genomic hyperparasitism

Question 27

In which phyla are enterprise elements widespread ing?

Answer 27

Ascomycota

Question 28

Where does the Voyageur transposon insert?

Answer 28

Into 5S rDNA
Contains candidate virulence factors whose copy number correlates broadly with pathogenic and saprophytic growth

Question 29

How do starships act as mediators of eukaryotic horizontal gene transfer?

Answer 29

Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components
Motifs of fungal tyrosine recombinases broadly group with bacterial tyrosine recombinases involved in HGT
Could be the first dedicated agents of active gene transfer in eukaryotes

Question 30

When do repeat-induced point mutations happen?

Answer 30

Occurs specifically in haploid parental nuclei that continue to divide by mitosis in preparation for karyogamy in ensuring meiosis
Detects duplications of chromosomal DNA above a certain length threshold and mutates cytosines on both strands of each DNA duplex in a pairwise fashion

Question 31

What does RIP generate a bias for?

Answer 31

AT-richness

Question 32

Why can’t you use second-generation sequencing to analyze TEs?

Answer 32

Detection of newly transposed events by transposable elements (TEs) from next-generation sequence (NGS) data is difficult, due to their multiple distribution sites over the genome containing older TEs