Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in<i>Oryza</i>

Transfer of chloroplast or mitochondrial DNA into the nuclear genome is a common phenomenon in many species. However, little is known about the evolutionary fate and mechanism of transfer of organellar DNA sequences in higher plants. We observe abundant insertions of organelle DNA into the nuclear genomes of 22 genome assemblies across seven <i>Oryza</i> species and further categorize nuclear organelle DNA (NORG) into 3406 orthologous groups. Analysis of the whole-genome resequencing data from 3458 <i>O. sativa</i>, <i>O. glaberrima</i>, and <i>O. barthii</i> accessions indicate that NORGs have intra- and inter-population variability owing to sequence loss and transposon insertion during evolution. Our results also suggest that NORGs have been continuously produced during the evolution of <i>Oryza</i>, and both double-strand break repair pathways and replication-based mechanisms play important roles in integrating organelle DNA into the nuclear genome. Further investigation indicates that complex NORGs are formed through single mutational events before or during the insertion process via ligation of multiple plastid and/or mitochondrial DNA with each other. In summary, this work provides novel insights into the process of endosymbiotic DNA transfer and its role in reshaping genome variation and plant genome evolution.