Genomes and Genomics 3

Techsession 7 2007

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Molecular Phylogenetic Analysis:

Horizontal Gene Transfer, or

Are there bugs in our genome?

Mark Blaxter

this file is at http://www.nematodes.org/teaching/genomics/Tech7/tech7_top.html
The lecture notes are here.

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Read through this schedule BEFORE starting to answer any of the questions: there are nuggets of useful information throughout...

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1: Horizontal gene transfer in Prokaryotes

2: Horizontal gene transfer in the Human Genome?

3: Investigating possible HGT events in the Human Genome

4: The N-acetylneuraminate lyase gene from Homo sapiens (Hs-anl)

5: Finding homologues of Hs-anl in other organisms

6: The N-acetylneuraminate lyase gene of the protozoan pathogen Trichomonas vaginalis (Tv-anl)

7: Finding homologues of Tv-anl in other organisms

8: Aligning a selected set of N-acetylneuraminate lyase proteins

9: Reviewing the alignment

10: Maximum parsimony analysis of the alignment

11: Bootstrap analysis of the best maximum parsimony tree

12: Neighbour-joining analysis of the alignment

13: Bootstrap analysis of the best neighbour-joining tree

14: Comparing the phylogenetic trees, and coming to a conclusion

15: References and further reading

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1: Horizontal gene transfer in Prokaryotes

Horizontal gene transfer (also known as lateral gene transfer; abbreviations are HGT or LGT) is the exchange of genetic material by two organisms that are not of the same biological species.

HGT is commonly observed in the genomes of bacteria and archaea, particularly of DNA segments encoding genes that specify "exotic functions" such as

* virulence factors

* antibiotic production

* antibiotic resistance

* restriction-modification systems

* specialised biochemical pathways

The prevalence of HGT in the prokaryotes has led some to suggest that the evolution of these organisms should be viewed as a reticulated net rather than a tree. However, despite HGT, the majority of the genes in any prokaryote genome have congruent evolutionary histories, and it is therefore possible to construct a robust bacterial phylogeny. Genes with evolutionary histories that disagree with this are candidate HGT events.

In prokaryotes, HGT events in the recent past can often be recognised because they have a GC bias or codon usage that differs significantly from the "host" genome. More ancient HGT events are harder to spot using these clues, as incorporated genes are relatively rapidly selected to have GC contents and codon biases more similar to their host's. In these cases, the ONLY evidence for HGT is the phylogenetic incongruence between the candidate HGT gene and the majority of the host genome.

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