Genomes and Their Evolution Flashcards
What is genomics?
- The study of genomes
- Involves analysis of whole sets of genes and their interactions
What is transcriptomics and proteomics?
The study of entire sets of RNA molecules and proteins
General properties of genomes
- Genome size, number and gene density vary within and between eukaryotes and prokaryotes
- Alternate splicing increases protein diversity without increasing genes
- Non-coding DNA is not necessarily non-functional
What is high-throughout sequencing?
Generate enormous amounts of data very rapidly
Illumina Advantages
- High accuracy
- Low error rate
Illumina Disadvantages
Short read length makes genome assembly difficult
Pacific Biosciences and Nanopore Advantages
Long read length improves genome assembly
Pacific Biosciences and Nanopore Disadvantages
- Lower accuracy
- Higher error rate
What is a microbiome?
The collective genomes of all microorganisms living in an environment
What its metagenomics?
- Study of the microbiome using high-throughout sequencing
What is ancient DNA?
- DNA isolated from ancient samples
- Can be sequenced
What is bioinformatics?
The use of computer software to analyze sequencing data
What is gene annotation?
Prediction of genes in genome sequencing and the function of the gene products
What is systems biology?
- It aims to understand whole cellular systems
- Goal of being able to predict biology
What are genome-wide association studies?
- A method to associate genetic variation across a population with specific phenotypes
- Can be used to identify genomic regions associated with disease risk or other traits
What accounts for 1.5% of the human genome?
- DNA sequences (exons) coding for protein, rRNA or tRNA
What accounts for 25% of the human genome?
- Gene-related DNA, including introns and regulatory elements
What accounts for the rest of DNA?
- non-coding DNA
- Repetitive elements
- Unique sequences
What are transposable elements?
- A segment of DNA that can move around and within the genome of a cell
- 20-50% of mammalian genomes
What is a transposon?
- Moves via a DNA intermediate
- Copy-and-paste mechanism of movement
What is a retrotransposon?
- Moves via a RNA intermediate
- Copy-and-paste mechanism
- In eukaryotes, retrotransposons are more common than transposons
Alu Elements
- About 300 nucleotides long
- account for 10% of the genome
- Help regulate gene expression
LINE-1 retrotransposons
- About 6500 base pairs long
- About 17% of the genome
- Contribute to neuron development
Transposable elements and evolution
- Can facilitate chromosomal translocations by providing sites for unequal homologous recombination leading to gene movement
- Disrupt genes, or modify rates of transcription
- Most changes are harmful, sometimes provide a benefit
Why is there repetitive DNA?
Due to errors in DNA replication or recombination
What are large-segment duplications?
Scattered copies of long sequences, copied from one region of the genome to another
What is simple sequence DNA?
- Tandemly repeated sequences
- Each repeat is 2 to 500 nucleotides long
- Found at telomeres and centromeres
What is a short tandem repeat?
- Simple sequence DNA with each repeat being 2 to 5 nucleotides long
Genome rearrangement affect?
Usually harmful but may provide benefit
What do translocations and fusions cause?
- Alterations in chromosome structure
- Contributes to the emergence of new species
What does polyploidy mean?
- When there are 3 copies of chromosomes
- Normally lethal but not always
- More common in plants, can lead to a new species
What causes polyploidy?
Duplication of entire chromosome sets via nondisjunction
How can polyploidy lead to a new species?
One set of genes provides essential functions while the other set(s) diverges through mutation
What happens when there is unequal crossing over during meiosis?
- Lead to duplication and deletion of chromosomal regions
What happens if DNA polymerase slips during DNA replication?
- Small duplications or deletions
- Contributes to changes in repeat numbers in short tandem repeats
What are multigenerational families?
- Collections of two or more similar genes with a common origin
- Usually clustered and often have RNAs as their final product
Evolution of the global multigenerational families
- Includes the alpha-globin and beta-globin gene families originating from a single ancestral gene
How were the global multigene families formed?
By duplications followed by a mutation leading to functional diversification
Evolution of genes with new functions
- Lysozyme breaks bacterial cell walls
- alpha-lactalbumin regulates milk production in mammals
- Alpha-lactalbumin evolved from a duplicated lysozyme gene with mutations
