genomics 2

orthologs

homologous genes at the same genetic locus in different species, evolutionarily from a common ancestor

paralogs

homologous genes at different loci in the same species, having arisen from gene duplication

phylogenetic inference of vitellogenin (egg yolk) gene

• monotremes (platypus) have one copy and lay eggs

• eutherians (mammals other than monotremes and marsupials) have no copies of the gene and do not lay eggs

• common ancestor of mammals and birds (and chickens) have 3 copies of the gene, suggesting that the ancestral gene was present originally and then lost in other mammals

• presence of traces of gene in mammals supports hypothesis that two copies were lost in synapsids, then eutherians lost the final one

sequence comparison within genome

can identify families of related genes

• encode proteins of similar amino acid sequence

• members can be functionally redundant or have independent functions

• presumably from ancestral gene duplication

human keratin-associated protein 1 family

• involved in the structure of human hair fibers

• thought to have arisen through gene duplication during evolution

dog genome project

• comparing genomes from different dog breeds to understand the genetic bases for their differences

• informs research into human health and health

• identified genes affecting dog size, leg length (extra copy of FGF4 gene in short-legged), length, texture, and curl of dog’s coat, sociability (more than wolves)

comparison of human genomes

• identifying genetic basis of a trait (ex: mutations in MC4R gene leading to obesity by preventing sense of fullness)

• forensics

• second site mutations being protective against disease

reveal of “parent-child” relationships with genome comparison

• individuals in 23andMe database screened, “parent-child duos” identified using “identity by descent”

• 199 individuals found that have two copies of a chromosome from one parent and no copies of that chromosome from the other parent (uniparental disomy)

uniparental disomy

• two copies of a chromosome from one parent and no copies from the other parent

• can arise from nondisjunction at either first or second division followed by trisomy rescue in embryo

• certain chromosomes are more or less likely to be found in UPD (either maternal or paternal)