Sequencing & Assembly
Essembling a genome without a reference genome
What is De Novo Sequencing?
All the DNA sequences that occur in a species
What is Pan Genome?
Recombination rate between loci and when r=0 it means the loci are tight.
What is r and what does it mean when r is zero?
Reduction in fitness of progeny from matings between closely related individuals relative to the fitness of progeny from matings between unrelated individuals
What is inbreeding depression?
More than 8 hemoglobin genes in humans and 1000 olfactory genes resulted from this.
What is the whole gnome duplication event?
A partial assembly of fragments into a contiguous stretch of sequence
What is Contig?
Usually non-functional, derived via mutational degeneration of genes
What is Pseudogenes?
This symbol measures deviation from random association between alleles at different loci.
What is D ( coefficient of gametic disequilibrium)?
Matings between closely related individuals.
What is inbreeding?
A group of closely related genes with similar functions.
What is a gene family?
Average number of times the nucleotide at each position has been independently determined
What is coverage?
Duplication of exon(s) of a coding region, followed by transfer to another coding region
What is Exon Shuffling?
When this equals zero, alleles at two loci are randomly associated in a population.
What is D=0, or gametic equilibrium?
When an individual receives two copies of the same allele that was present in a single common ancestor of its parents
What is identical by descent (IBD)?
A third whole-genome duplication occurred in this lineage.
What is the ray-finned fish lineage?
The study of the structure and function of entire nucleotide sequences isolated and analyzed from all the organisms (typically microbes) in a bulk sample
What is Metagenomics?
The duplication of a single gene within a genome which producing multiple copies of that gene
What is gene duplication?
This equation predicts the value of D in the next generation.
What is D' = D(1-r)?
What is runs of homozygosity (ROH)?
Name one potential evolutionary advantage of Gene duplication
What is giving rise to Gene families/allowing genes to diversify in function/providing a backup copy?
Most or all of the nuclear DNA sequence from a single individual assembled into a continuous segments.
What is Assembled reference genome?
Containing more than one copy of a set of chromosomes
What is Polyploidy?
Name one cause of gametic disequilibrium besides physical linkage.
What is nonrandom mating, family structure/inbreeding, or hybridization?
What is Fp (pedigree inbreeding coefficient)?
Recombination and time cause this to decline in populations.
What is the decay of gametic disequilibrium (D)?