Inferring Recombination Events in Plant Mitochondria Using High- Throughput Sequencing Data

CAROLINA L. GANDINI; LAURA E. GARCIA; CINTHIA C. ABBONA; SERGEI KUSHNIR; DANNY GEELEN; M.V. SANCHEZ- PUERTA

Mendoza

Congreso; 10th Argentinian Conference on Bioinformatics and Computational Biology; 2019

A2B2C

Angiosperm mitochondria genomes (mtDNA) exhibit extremely high rates of recombination and sequence rearrangement. Moreover, the ability to incorporate foreign sequences into their genomes is thought to be mediated by homologous recombination (HR). An interesting way to study recombination in mtDNA consists of the generation of somatic hybrids. Our lab has recently studied two hybrids between the Solanaceae Hyoscyamus niger and Nicotiana tabacum. They found that the resulting mtDNA was highly chimeric and occurred entirely via HR mechanisms, mostly by the break-induced replication (BIR) pathway. In this study, we analyzed the recombination map of a somatic hybrid between the Solanaceae Physochlaina orientalis and N. tabacum. To do so, we performed high-throughput sequencing of the hybrid genome and we developed a novel bioinformatic strategy that infers recombination events by analyzing genome switches and single nucleotide polymorphisms (SNPs) within paired-end reads. Using this pipeline, we were able to detect 55 HR events occurring, as in the H.niger-N.tabacum hybrids, mostly by the BIR pathway. Interestingly, some recombination events seem to have happened in the same homologous region independently. By mapping the hybrid reads over the parental genomes, we estimate that the hybrid mtDNA have a minimum size of ~749 kb, consisting in ~404 kb (~59%) of P. orientalis and ~345 kb (~80%) of N. tabacum mtDNAs. The hybrid mtDNA possesses the same gene set that their parents, with a total of 37 protein-coding genes and three ribosomal genes. 20 of them were inherited from N. tabacum and 17 from P. orientalis. In addition, five (atp1, atp4, nad6, rps3, rps4) were chimeric, and only two (atp4, nad6) appears to be duplicated. These results are slightly different from the ones of the H.niger-N.tabacum hybrids, were the contribution of tobacco was much higher. The only chimeric gene shared by the three hybrids was atp1.Our technique allowed us to study recombination events without the need to assemble the hybrid mtDNA. However, further analysis needs to be done to deeper understand the mechanism of mitochondrial recombination.