  Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic
material can be transferred between species and integrated into the genome via
homologous or illegitimate recombination. There is little reason to imagine
that the units of transfer correspond to entire genes; however, such units have
not been rigorously characterized. We examined fragmentary genetic transfers in
single-copy gene families from 144 prokaryotic genomes and found that
breakpoints are located significantly closer to the boundaries of genomic
regions that encode annotated structural domains of proteins than expected by
chance, particularly when recombining sequences are more divergent. This
correlation results from recombination events themselves and not from
differential nucleotide substitution. We report the first systematic study
relating genetic recombination to structural features at the protein level.
