It's not so explicit in the publications I have encountered...
Salvador, there are many examples of significant difference of particular gene trees and genome trees, especially for pathogenicity-associated genes. In some cases, horizontal transfer of the genes was suggested. Usually, such "atypical" gene tree can place the studied strains into different species group.
Look:
http://aem.asm.org/content/early/2014/12/15/AEM.03000-14.full.pdf
http://onlinelibrary.wiley.com/doi/10.1111/nph.12397/pdf
Most bacteria experience at least some horizontal gene transfer, usually between relatively related species (Salmonella-Shigell-Escherichia for example) but also between quite distantly related organisms. If you choose "housekeeping" genes sich as robosomal RNA genes, ribosomal protein gene, DNA Polymerase and so on, the gene trees usually agree with the majority of the genome. But as Alex noted, many other genes are very often transferred between species.
Hi Salvador, The first source of discordance between a genome tree and a gene tree are Horizontal Gene Transfers: you can detect them in bacteria and eukaryotes as well. But you may also have genes facing selection, in some population which may give distorded / discordant phylogenies. Best regards.
Jean-Luc
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