I need to show the species tree in my paper in order to illustrate a HGT event of a gene of interest. All of the organisms I am focusing on are bacteria and have complete genome sequences in public database. Should I build a species tree for them myself based on rRNA sequences or should I find their taxonomic relationship somewhere else from previous studies? Thanks!
1 answer
You can do either -- just be clear to what you have done in your figure.
Most phylogenetic trees I see (on the basis of what you have described) are MLST based phylogenetic trees that were constructed by picking a dozen (or more) well documented genes of interest (or phylogenetically informative genes). You then can establish some statistics for your HGT event by using numerous other genes to benchmark timing by sequence divergence, genome location, etc.
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