  The widespread presence of antibiotic resistance and virulence among
Staphylococcus isolates has been attributed to lateral genetic transfer (LGT)
between different strains or species. However, there has been very little study
of the extent of LGT in Staphylococcus species using a phylogenetic approach,
particularly of the units of such genetic transfer. Here we report the first
systematic study of the units of genetic transfer in 13 Staphylococcus genomes,
using a rigorous phylogenetic approach. We found clear evidence of LGT in 26.1%
of the 1354 homologous gene families examined, and possibly more in another
17.9% of the total families. Within-gene and whole-gene transfer contribute
almost equally to the discordance of these gene families against a reference
phylogeny. Comparing genetic transfer in single-copy and in multi-copy gene
families, we found little functional bias in cases of within-gene (fragmentary)
genetic transfer but substantial functional bias in cases of whole-gene
(non-fragmentary) genetic transfer, and we observed a higher frequency of LGT
in multi-copy gene families. Our results demonstrate that LGT and gene
duplication play an important part among the factors that contribute to
functional innovation in staphylococcal genomes.
