Chenbo Gong1, Yicheng Huang1, Mengmeng Liu1, Yong Zhou2, Yinwei Xu1, Nahed Mohammed2, Xintong Qiao1, Andrea Zuccolo2, Weibo Xie1, Rod A. Wing2,3, Jianwei Zhang1, Fei Zhou1 and Yongjun Lin1 1National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; 2Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955‐6900, Saudi Arabia; 3Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA Corresponding authors: rod.wingkaust.edu.sa, jzhangmail.hzau.edu.cn, zhoufeimail.hzau.edu.cn, yongjunlinmail.hzau.edu.cn Abstract

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 Oryza species and further categorize nuclear organelle DNA (NORG) into 3406 orthologous groups. Analysis of the whole-genome resequencing data from 3458 O. sativa, O. glaberrima, and O. barthii 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 Oryza, 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.

Received May 27, 2024. Accepted March 27, 2025.