Genome Evolution Lecture 15

Flashcards about Genome Evolution

What is the focus of genome architecture in genome evolution?

The structure and organization of the information encoded in the genome.

What is the C-value?

The amount of DNA in a haploid cell, such as a gamete, measured in picograms.

What is the C-value paradox?

The observation that the amount of DNA in an organism does not correlate with its complexity.

What are mobile genetic elements?

Selfish DNA that replicates and inserts itself into the host genome.

What is the role of mobile genetic elements in mutation?

They can be a major force of mutation, disrupting the genome or accumulate as junk DNA.

What is the difference between genes in prokaryotes and eukaryotes?

Eukaryotes have introns in the coding regions, separating exons, which is different from prokaryotes.

What are operons and where are they found?

Functional groups of genes organized in prokaryotes, containing co-regulated genes controlled by a single regulatory element.

What is the typical definition of 'function' for intergenic DNA?

Being evolutionarily conserved and under selection.

Intron effects on eukaryotes

-contain enhancers and silencers to modify gene expression and regulatory mechanisms.

Examples of Junk DNA

1) larger repeat regions

2) pseudogenes

3) mobile genetic elements

Transposable Elements and Effective Population Size

• with large Ne, selection is effective

• with small Ne, genetic drift more effective

What are Class I transposable elements?

Retrotransposons that transport via a copy-and-paste mechanism using RNA as a transmission intermediate.

What are Class II transposable elements?

DNA transposons that transport via a cut-and-paste mechanism without an RNA intermediate.

What can DNA transposons take advantage of?

• can take advantage of ds gap repair during recombination

Autonomous TEs

• carry all genes necessary in replication

Non-autonomous TEs

• must be in presence of other TEs to use their products

• SINEs

What are the two main tools the genome uses against transposable elements?

Post-transcriptional silencing (Small RNA molecules) and Pre-transcriptional silencing (Methylation)

What do siRNAs do?

Silence TEs by binding to them.

• Ler allele in FLC gene

What is the role of methylation in fighting mobile genetic elements?

Host cells use methylation to prevent regions of the genome containing TEs from being transcribed.

How can TEs reprogram gene expression, referencing the wine-making grape color?

Insertion of a Gret1 LTR retrotransposon disabled expression of the Vvmby1 gene, causing a loss of color in the fruit.

How is mutation rate related to genome size in viruses, bacteria, and some archaea PROKARYOTES

Mutation rate decreases as genome size increases.

How is mutation rate related to genome size in most eukaryotes?

Mutation rate increases with genome size.

Lynch Hypothesis for mutation rates?

larger populations tend to have lower mutation rates due to stronger selection against deleterious mutations, interaction of selection and drift

What did Loh, et al. discover about mutation rates in E. coli strains?

Strains with high, but not highest, mutation rates took over in competition experiments for resources.

What is the primary method to acquire new genes?

Gene duplication.

What are whole genome duplications?

-polyploid genes: all chromosomes and their genes are duplicated

What are segmental duplications?

-duplicate small number of genes with unequal crossing over and TEs

What is nonfunctionalization?

A disabling mutation that destroys one of the gene copies after duplication.

• how pseudogenes occur

What is subfunctionalization?

The preservation of duplicate genes by partitioning gene function among the duplicate copies.

Adaptive Constraint in Sub functionalization

-2 or more phenotypes can’t be optimized at the same time, selection functions on 2 phenotypes independently

What is synteny?

The preservation of gene order, or gene neighborhoods along the chromosome, through evolutionary time.

What are the two possible origins of alleles for new adaptations?

Adaption from standing genetic variation and adaption from new mutation.

What evidence supports the hypothesis that TTX resistance alleles arose independently in garter snakes?

-species of garter snakes showed resistance to TTX, convergent evolution so mutations evolved in different species independently

What are 3 possible limiting factors of genome size?

1) biochemical and energy costs

2) energy requitements

3) geometric and time constraints