DNA Flashcards
What does DNA alignment tell us?
Aligned positions are homologous
What does homology mean?
Likeness in structure between parts of different organisms due to evolutionary differentiation from a corresponding part in a common ancestor
In DNA barcoding, sequences that are 97% or more similar to each other are clustered into what?
Operational taxonomic units (OTUs) or amplicon sequence variants (ASVs)
Which attributes does a good gene (or gene marker) have?
Found across all of the pertinent tree of life
Not too conserved, not too variable
Variability should distinguish between each species
Relatively more abundant in the cell = easier to sequence if you have very little DNA
Why is CO1 (mitochondrial DNA) not a great marker to use for DNA barcoding?
Not every fungus has mitochondria (microsporidia lack them)
Lack of resolution
Lack of prior work on CO1 in fungi
What is rDNA present as in fungi?
As repeats on the genome
What is the 5.8S unit of rDNA?
It is a highly conserved unit with little variation between members of a family
What are the 18S and 25S units of rDNA?
They are two larger subunits that are more variable than 5.8S, but still quite conservative
What is the ITS unit of rDNA?
Internal transcribed spaces that sit between the small and large ribosomal subunits
More variation
What are housekeeping genes?
Genes that are involved in basic cell functions, that all cells have
What are cryptic species?
DNA data supports the existence of genetically distinct species
Traits under selection might not be easy to phenotype/visualize
What happens if ribosomal repeats are not identical?
Heterozygosity
Can you use ITS for population studies?
No, it is not variable enough
It is good for variability in DNA sequences from species to species, but not amongst individuals in a population
What are microsatellites?
Short-tandem repeats
