Genetics post-exam 4 material

Contigs

Overlapping sequences that can be assembled to make larger pieces

Consensus sequence

A sequence that has pieces from multiple sequences

WGS sequence

Traditional or next generation, method for constructing the human genome

Genomic libriaries

Collections of randomly sampled DNA fragments that are cloned into plasmids. Used in traditional WGS sequencing

Steps for next generation sequencing

* Adaptor sequences attached to small DNA fragments (reads)
* Amplify fragments via flow cell
* Sequencing by DNA synthesis (uses DNA polymerase) with dyes

Illumina sequencing

2nd generation sequencing that produces lots of data, assembly of the genome is challenging

PacBio

3rd generation sequencing that produces few, long reads and is easier to assemble

Repetitive elements

Short, repetitive tracks for many many base pairs. Primary challenge to sequence assembly

Genome annotation

identification of all the functional elements of a particular genome

Open reading frames

DNA segment with start and stop codons

Complementary DNA

cDNA, derived from mRNA. Needed for annotation because we can’t sequence RNA

Proteome

Inventory of the proteins a genome encodes

transposable elements

repetitive DNA sequences that can copy, cut, and paste themselves around the genome

Pseudogenes

Genes that have mutated and no longer function

Phylogeny

the evolutionary history of a group depicted by a tree, can be inferred from genomic data

Homologs

Any genes that share ancestral history

Orthologs

Genes found in different species that are related due to originating from an ancestral species

Paralogs

Multiple genes in 1 species that are related due to a gene duplication event in the past

Synteny

Regions of different species’ genomes that are arranged in similar blocks due to common ancestry. Useful for studying model organisms

Barbara McClintock

Discovered transposable elements in Maize

Nonautonomous transposable element

Ds (disassociation) locus, can move around the genome, leading to different phenotypes

Activator sequence

Ac locus, encodes Transposase

IS elements

 can move around but can't take other genes with them

Transposons

Can move around and take other genes with them

transposase

enzyme required for movement

Composite transposons

Can carry other genes around with them. Has 2 IS elements, each with transposase genes

Replicative transposition

Transposons replicate, number of transposons increases

Conservative transposition

Transposons cut and paste, number of transposons does not increase

Retrotransposons

Derived from retroviruses, all have reverse transcriptase

Reverse transcriptase

Enzyme that converts mRNA to cDNA

P elements in drosophila

Similar to bacterial IS elements, ends are short inverted repeats that flank a transposase gene.

Individuals with these elements have silencing factors in their cytoplasm

Hybrid dysgenesis

Production of biologically deficient hybrids from certain crosses

C-value paradox

Genome size varies dramatically among eukaryotes, but this is not explained by complexity

Haplotype

A haploid segment of a chromosome defined by its sequence

Haplotype network

Graphical representation of haplotype relationships

Hardy Weinberg rules

Random mating only, no selection, free mating, no mutations, infinite population size

Genetic drift

Allele frequency change due to sampling error

Fixed allele

Allele frequency in population of 100%