Abstract Somatic hybrids between distant species offer a remarkable model to study genomic recombination events after mitochondrial fusion. Recently, our lab described highly chimeric mitogenomes in two somatic hybrids between the Solanaceae Nicotiana tabacum and Hyoscyamus niger resulting from interparental homologous recombination. To better examine the recombination map in somatic hybrid mitochondria, we developed a more sensitive bioinformatic strategy to detect recombination activity based on high-throughput sequencing without assembling the hybrid mitogenome. We generated a new intergeneric somatic hybrid and re-analyzed the two Solanaceae somatic hybrids. We inferred 213 homologous recombination events across repeats of 2.1 kb on average. Most of them (∼80%) were asymmetrical, consistent with the break-induced replication (BIR) pathway. Only rare (2.74%) non-homologous events were detected. Interestingly, independent events frequently occurred in the same regions within and across somatic hybrids, suggesting the existence of recombination hotspots in plant mitogenomes. BIR is the main pathway of interparental recombination in somatic hybrid mitochondria. Likewise, under the fusion compatibility model of mitochondrial horizontal transfer, foreign mitochondria fuse with those in the recipient cell and their genomes likely recombine via BIR, resulting in the integration and/or loss of mitochondrial DNA. Findings of this study are also relevant to mitogenome editing assays. Highlight We show that the chimeric mitochondrial genomes of somatic hybrids result from one of the three described homologous recombination pathways (BIR), mimicking the fusion compatibility model for plant HGT.

Break-induced replication is the primary recombination pathway in plant somatic hybrid mitochondria: a model for mt-HGT