Bacillus subtilis recipient cells transform for 20 cycles with genomic DNA of four donor species and the whole genome of the resulting hybrids is sequenced. Orthologous recombinations, deletions and insertions are detected for two time points. We verify that the assay is non-selective by showing that the accumulation of replacement events does not increase the mean fitness. We investigate the identities of replaced segments and analyse their lengths and the accumulation over time. In conclusion, we find that the sequence divergence and genome architecture poses a strong barrier to gene transfer in a cross-species scenario.