lecture 10, Horizontal gene transfer- compatibility mode Flashcards
what is Horizontal Gene Transfer (HGT)
Horizontal Gene Transfer (HGT) is the exchange of genes between different strains or species.
HGT is an important evolutionary mechanism in…
prokaryotes and the fungal kingdom
How many genes has S. cerevisiae acquired from HGT
S. cerevisiae has acquired 13 genes via HGT
where did S. cerevisiae acquire these genes from?
from bacteria since it diverged from its close relative A. gossypii.
what % of the S. cerevisiae genome do these 13 genes correspond?
less than 1%
What functional innovations do these 13 genes contribute to?
- synthesise biotin,
- grow under anaerobic conditions
- utilise sulphate from several organic sources.
What fungus has acquired bacterial metabolic genes from HGT
C. parapsilosis
How had HGT caused Pyrenophora
The acquisition of a toxin gene (ToxA) by Pyrenophora tritici-repentis from Stagonospora nodorum resulting in Pyrenophora infestations of wheat.
how can HGT be detected
- 1) Similarity based approach.
- 2) Divergent GC content.
- 3) Divergent codon usage patterns.
- 4) Phylogenetic reconstruction.
what is the disadvantages of
* 1) Similarity based approach.
* 2) Divergent GC content.
* 3) Divergent codon usage patterns.
* 4) Phylogenetic reconstruction.
They give false positives
Detecting HGT by examining their Patchy phyletic distribution, look at slide 8A
if gene of interest is not found in closely related relatives and orthologs can only be located in distantly related species.
Detecting HGT by examining their Gene of interest location look at slide 8 B
in conserved synteny block and absent from closely related species May also indicate a gene loss but similarity based searches can help validate if it is a potential HGT event or loss
Detecting HGT by examining their Phylogenetic inference look at slide 8 C
species gene tree on the right differs from gene tree on the left. Phylogenetic inconsistency can be used to detect HGT and also determine the donor species.
Detecting HGT by examining codon usage variations look at slide 8 D
native genes have a preferential codon usage pattern (blue dots), recently transferred genes have yet to improve to their new hosts genome and still display the codon usage pattern of their cognate genome.
Detecting HGT by examining variations in their GC content. look at slide 8 E
Variation in GC composition along a chromosome may indicate alien genetic material has recently been acquired. In this case the transferred DNA has a GC content lower than the recipient genome.
