Agrobacterium-derived DNA sequences in phylogenetic studies of plants

One of the main methods for obtaining transgenic plants is Agrobacterium-mediated transformation. This process relies on the ability of certain soil bacteria, specifically from the genera Agrobacterium and Rhizobium, to transfer and integrate a fragment of their plasmid into the chromosome of the recipient plant. This transferred DNA is referred to as T-DNA. Laboratory studies have demonstrated that whole plants can be regenerated from transgenic cells. It soon became evident that similar processes occur in nature, leading to the emergence of naturally transgenic plants, or natural GMOs. Thus, naturally transgenic plants possess homologues of the T-DNA genes from agrobacteria in their genomes (cellular T-DNA, or cT-DNA). These sequences are inherited through multiple sexual generations and retain their functionality. Furthermore, the potential for using newly acquired plant sequences in phylogenetic studies has been established, as cT-DNAs are clearly defined, highly specific, and recognizable DNA fragments that differ from typical plant DNA sequences. They are not found in untransformed ancestors, and their integration at specific chromosomal sites marks a monophyletic group of species. This review highlights the diversity of cellular T-DNAs and their potential use as phylogenetic markers. It includes a description of the main methodological approaches to such studies and discusses specific examples that clarify controversial points in the phylogeny of the genera Nicotiana, Camellia, Vaccinium, and Arachis. An important aspect of phylogenetic analysis based on cT-DNA is the assembly of individual alleles, which enables the tracking of interspecific hybridization events. This approach demonstrated the incomplete process of speciation within the Thea section of the genus Camellia and confirmed the role of interspecific hybridization in the breeding of North American blueberries. The review also addresses the dating of transformation events based on cT-DNA, which are organized in the form of imperfect repeats, as well as the application of phylogenetic studies to investigate the biodiversity of agrobacterial T-DNA genes.