  Adaptation of bacteria occurs predominantly via horizontal gene transfer
(HGT). While it is widely recognized that horizontal acquisitions frequently
encompass multiple genes, it is unclear what the size distribution of
successfully transferred DNA segments looks like and what evolutionary forces
shape this distribution. Here, we identified 1790 gene family pairs that were
consistently co-gained on the same branches across a phylogeny of 53 E. coli
strains. We estimated a lower limit of their genomic distances at the time they
were transferred to their host genomes; this distribution shows a sharp upper
bound at 30 kb. The same gene-pairs can have larger distances (up to 70 kb) in
other genomes. These more distant pairs likely represent recent acquisitions
via transduction that involve the co-transfer of excised prophage genes, as
they are almost always associated with intervening phage-associated genes. The
observed distribution of genomic distances of co-transferred genes is much
broader than expected from a model based on the co-transfer of genes within
operons; instead, this distribution is highly consistent with the size
distribution of supra-operonic clusters (SOCs), groups of co-occurring and
co-functioning genes that extend beyond operons. Thus, we propose that SOCs
form a basic unit of horizontal gene transfer.
