Historical breeding reveals graph-based structure dynamics and intracellular DNA transfer in rice mitogenome

Plant mitochondrial genomes are characterized by extremely low sequence mutation rates yet extraordinarily high structural variability. That is the famous plant mitochondrial evolutionary paradox. Despite this pervasive structural plasticity, the mechanisms underlying evolutionary continuity remain poorly understood, particularly over short-term breeding histories. In this study, we analyzed ten cultivars sampled across modern japonica rice breeding history (1882–2011) using long-read sequencing and graph-based assembly. Within the documented rice lineage in among the samples, the core assembly master graph-based structure was conserved, whereas other two sampled breeding branches showed alternative graph connections consistent with repeat-mediated rearrangement. A variety Shennong265, classified as japonica from its nuclear background, yet whose mitochondrial genome clearly points to an indica maternal origin. In the nuclear genomes analyzed here, ultra-long organellar insertions (> 10 kb) showed a clustered distribution, with NUPTs concentrated on chromosome 4 and NUMTs enriched on chromosome 12. A 63-kb NUMT comprising six distinct mitochondrial segments was supported by ultra-long reads in Akitakomachi. That indicated there are multiple independent insertion events into a super large NUMT. By integrating analyses of structural variation and intracellular DNA transfer within a historical breeding framework, this study provides new insights into the evolutionary behavior of plant mitogenomes under artificial selection. It also establishes a foundation for understanding crop breeding history from a cytoplasmic perspective.