I have performed synteny based comparison of a pathogenome of interest (say X) against the remaining strains of same group. I have then performed domain analysis of putative genes of X and have considered genes which are unique in relation to other strains of the same group. Finally among these unique proteins, I got Ankyrin repeat (ANK) where I want to focus on. Literature says that pathogens have evolved by incorporating such repeats (ANK) from eukaryotic hosts as they help in inducing pathogenesis to the host. It is also seen that the ANK in pathogen X has an ortholog in host (with Divergence=0.8, BLAST E-value=1e-5), possibly this might be due to HGT events.
So now my query is how can I trace this HGT event from eukaryote to prokaryote with a bioinformatic approach to prove that X has obtained ANK repeat from the host organism? Or is there any other way to continue with, other then to prove the HGT event, for a publication.
HGT detection is quite complex and require phylogenetic analysis (tree building algorithm).
There are various review papers for concept building and deciding important factors for such work. I am mentioning only few, you can further build on these.
http://www.nature.com/nrmicro/journal/v3/n9/full/nrmicro1204.html
http://www.nature.com/nbt/journal/v22/n9/full/nbt1006.html
http://www.sciencedirect.com/science/article/pii/S0092867406001772
http://www.sciencedirect.com/science/article/pii/S136952740300119X
http://www.nature.com/nrg/journal/v6/n5/full/nrg1603.html (Check out the references for various important publication)
Lawrence JG:
Horizontal and Vertical Gene Transfer: The Life History of Pathogens.
Russell W, Herwald H (eds): Concepts in Bacterial Virulence. Contrib Microbiol. Basel, Karger, 2005, vol 12, pp 255-271
(DOI: 10.1159/000081699)
and so on ....
Publications on bioinformatics methods, pipeline and tools available are as follows. I am mentioning few and there are numerous publications already there.
http://bib.oxfordjournals.org/content/6/4/394.abstract
http://www.sanger.ac.uk/resources/software/alien_hunter/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829038/
http://www.biomedcentral.com/1471-2148/5/27
http://bioinfo.cs.rice.edu/phylonet/
http://www.lirmm.fr/~gambette/PhylogeneticNetworks/show.php?keyword=Program%20HorizStory&op=n
and so on ....
All the Best.
Thank you Surendra Kumar and Rohan Chaubal. Will carry on with your ideas and update....
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