Genomes
and Genomics 3
Techsession 7
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.
Read through
this schedule BEFORE starting to answer any of the questions: there
are nuggets
of useful information throughout...
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
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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