SU Bacterial genome evolution

Question 1

Aphids

Answer 1

• phloem sap feeding pests
• because they feed on sap they contain specific symbionts
• Buchnera is a genus of endosymbiotic bacteria that primarily reside within the specialized cells of aphids and are vertically transmitted to offspring

Question 2

Genome size

Answer 2

• vary enormously
  Factors driving genome size:
• Location:
  spiecies that live in different places have different sizes, inside animals have smaller, free living bacteria have larger. As bigger genomes are found in species in more complex habitats (they do more “stuff”)
• population size:
  small, Fewer new mutations, more genetic drift (random changes in the frequency of alleles (gene variants) in a population over time)), more deleterious mutations (fix by drift)
  large, more new mutations (more diversity) and natural selection more effective, few deleterious mutations (purged by natural selection)

deleterious mutations, genetic alterations that have a harmful effect on an organism’s fitness, survival, or reproduction

Question 3

Muller’s ratchet

Answer 3

Stochastic (random) loss of the wild type genotype by genetic drift through asexual reproduction. Once deleted it will never recover only when back transforming or sudden sexual reproduction that can reintroduce the wildtype gene
- sexual reproduction defeats mullers ratchet early on in the process

Question 4

Streamlining hypothesis

Answer 4

Through natural selection non essential and non coding DNA gets removed improving reproductive benefit

The genome gets streamlined through natural selection, smaller genome size with less non-coding DNA and fewer non-essential genes -> reproductive benefit

Question 5

The Black Queen Hypothesis

Answer 5

evolutionary theory that describes a scenario where certain organisms may lose the ability to perform essential functions due to their reliance on other organisms for those functions

Evolution of dependancies through adaptive gene loss

Question 6

Overview genome sizes and EXTRA

Answer 6

Smaller genome can gain adaptive potential and become a bigger genome by:
- Gene duplications
- De novo gene birth: process by which new genes are formed from previously non-coding DNA sequences, rather than arising from the duplication of existing genes
- Horizontal gene transfer

Bigger genomes can lose genes for adapting to a specific niche to smaller genome by:
- Genetic drift: the change in frequency of an existing gene variant in the population due to random chance
- Psuedogenization: a gene loses its function and becomes a pseudogene, which is a non-functional segment of DNA that resembles a gene but has been rendered inactive
- Streamlining: most in free-living MO with high effective population size

Question 7

Horizontal (lateral) gene transfer

Answer 7

A process in which an organism transfers genetic material (DNA) to another cell that is not their offspring
* Transformation uptake and incorporation of free DNA from the environment
* Transduction foreign DNA is transfered into a cell by a virus or viral vector like bacteriophage
* Conjugation direct transfer of genetic material of plasmids (drug resistance) between bacterial cells through physical contact, typically mediated by a pilus

Phylogeny horizontal gene transfer understanding, it allows researchers to investigate how and why certain genes are transferred among species and to assess the implications of these transfers for evolution and adaptation.

Question 8

Pangenome

Answer 8

the complete set of genes within a species, encompassing both the core genome (what every induvidual of this species contains) and the accessory (or variable) genome.
- open pangenome, small core genome and large accessory genome. Large population size, diverse community interactions
- closed pangenome, large core genome and small accessory genome. Limited community interactions, small population size

Effects on pangenome size, host reliance, host location, motility, effect on host, host- or free- living (free living more open pangenome and bigger genome then host associated), genome size, effective population size

closed: Definition: A closed pangenome is characterized by a stable set of genes that do not significantly increase with the addition of more strains or individuals. This means that most of the genes are already present in the initial strains analyzed, and new strains contribute very few additional genes.
Open: An open pangenome is characterized by a continuously expanding set of genes as more strains or individuals are analyzed. This means that each new strain tends to contribute additional unique genes to the overall genetic repertoire of the species