Hai Liu, Weiqing Wang, Jiani Li, Yaxi He, Shengyuan Cao, Zenghui Hu, Yuanyuan Liu, Jie Hao, Yuehong Yan, Léon Otten, Ke Chen
Developed a method to detect cT-DNAs in plant genomes, identifying 2614 nGMO species, primarily eudicots, but also in mosses and ferns. Detected cT-DNAs in 82 mosses and 75 ferns, indicating Agrobacterium can transform early land plants, and found mini T-DNAs with a single opine synthase gene in these species. The findings reveal an ancient role for mini T-DNAs in natural horizontal gene transfer among early land plants, with potential implications for plant evolution and genetic diversity.
Agrobacterium transfers DNA into plant cells, leading to tumors, hairy roots (HR), and natural genetically modified organisms (nGMOs). Transferred DNAs (T-DNAs) from agrobacteria and T-DNA-derived cellular T-DNAs (cT-DNAs) from nGMOs vary considerably and may carry up to 15 different genes. Among these, opine synthase (ops) genes encode the synthesis of opines used as nutrients by the agrobacteria. Earlier studies predicted large numbers of naturally transformed plant species, but only few have been identified and studied so far. We therefore developed a general method to detect cT-DNAs in all publicly available whole genome sequences (WGS) and Sequence Read Archive (SRA) data from land plants. To avoid false positives, we only retained DNA sequences coding for T-DNA proteins. A total of 2614 nGMO species were identified, most are eudicots. However, cT-DNAs were also found in 82 mosses and 75 ferns, showing that Agrobacterium can also generate natural transformants among the early land plants. Analysis of 149 cT-DNA maps revealed different types of T-DNAs. Most notably, these included small T-DNAs (mini T-DNAs) with a single opine synthase gene. Mini T-DNAs are not expected to induce tumors or HRs. The predominance of mini cT-DNAs in mosses and ferns, and the presence of more complex cT-DNAs in spermatophytes, indicate that mini T-DNAs represent the earliest types of T-DNA. Our study also detected unusual T-DNA integration patterns, with multiple copies spread out over several hundreds of kilobases.