Genomes Flashcards
What are the two main ways to determine genome size?
Estimate of nuclear particle size
Direct sequencing
What is the process of Feulgen staining in assessing genome size?
HCL followed by Schiff reagent and ethanol wash
DNA should turn red
Intensity of reaction following hydrolysis of DNA is measured by a microdensitometer
What is the process of flow cytometry in assessing genome size?
Laser detection of particle size in suspension
What are smaller genomes associated with?
Forms tighter host associations
What are larger genomes associated with?
Mobile DNA content
What are the characteristics of microsporidia?
Unicellular parasites
Lack motile structures
Endospore contains chitin
Mitochondria are replaced by mitosomes
What are mitosomes?
Lacks a genome and function is unclear
Has some of the proteins found in mitochondria
What is the polar filament of microsporidia?
Harpoon mechanism
It is coiled and ready to deploy to infect cells, the tube transports contents to infected cell
What are the two ways that microsporidia can develop in humans?
Proliferation within cytosol or proliferation within parasitophorous vacuoles
How are DNA sequences determined using first-generation technology (Sanger sequencing)
Infer nucleotide identity using dNTPs then visualize with electrophoresis
Short-sequence reading
How are DNA sequences determined using second-generation technology?
High throughput from the parallelization of sequencing reactions
Short-sequence reading
How are DNA sequences determined using third-generation technology?
Sequence native DNA in real-time with single-molecule resolution
Long-sequence reading
What are transposable elements?
DNA sequences that can move in the genome, can represent up to 85% of the genomic content
What are class I (retrotransposans) TEs?
Copy and paste
What are class II TEs?
Cut and paste
What is the effect of TEs on fungal genomes?
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
What do genomic rearrangements sometimes produce?
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
What are the functions of Spok protein?
It performs both killing and resistance functions
How do Spok genes violate Mendelian laws?
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
What are Spok blocks?
Collected Spok elements that can move around and can be present in at least 4 different genomic locations
Why the varying positions of Spok blocks?
The Spok block is not only capable of meiotic drive but it is also capable of transposition
What is the Enterprise?
One Spok block that is contained in a giant tyrosine-recombinase mobilized DNA transposon
What does Kirc contain?
A domain called DUF3435 which is found to overlap in motif with tyrosine recombinases
How can TEs with a spore-killing-related crypton (Kirc) occur?
With or without Spok block as cargo
What is Kirc associated with?
Duplicated genes in ascomycetes
What happens with the Spoks are captured by the Enterprise?
Genomic hyperparasitism
In which phyla are enterprise elements widespread ing?
Ascomycota
Where does the Voyageur transposon insert?
Into 5S rDNA
Contains candidate virulence factors whose copy number correlates broadly with pathogenic and saprophytic growth
How do starships act as mediators of eukaryotic horizontal gene transfer?
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
When do repeat-induced point mutations happen?
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
What does RIP generate a bias for?
AT-richness
Why can’t you use second-generation sequencing to analyze TEs?
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
