Conservation of an Agrobacterium cT-DNA insert in Camellia section Thea reveals the ancient origin of tea plants from a genetically modified ancestor

Abstract

IntroductionMany higher plants contain cellular T-DNA (cT-DNA) sequences from Agrobacterium and have been called “natural genetically modified organisms” (nGMOs). Among these natural transformants, the tea plant Camellia sinensis var. sinensis cv. Shuchazao contains a single 5.5 kb T-DNA fragment (CaTA) with three inactive T-DNA genes, with a 1 kb inverted repeat at the ends. Camellia plants are allogamous, so that each individual may contain two different CaTA alleles.Methods142 Camellia accessions, belonging to 10 of 11 species of the section Thea, were investigated for the presence of CaTA alleles.Results discussionAll accessions were found to contain the CaTA insert, showing that section Thea derives from a single transformed ancestor. Allele phasing showed that 82 accessions each contained two different CaTA alleles, 60 others had a unique allele. A phylogenetic tree of these 225 alleles showed two separate groups, A and B, further divided into subgroups. Indel distribution corresponded in most cases with these groups. The alleles of the different Camellia species were distributed over groups A and B, and different species showed very similar CaTA alleles. This indicates that the species boundaries for section Thea may not be precise and require revision. The nucleotide divergence of the indirect CaTA repeats indicates that the cT-DNA insertion took place about 15 Mio years ago, before the emergence of section Thea. The CaTA structure of a C. fangchengensis accession has an exceptional structure. We present a working model for the origin and evolution of nGMO plants derived from allogamous transformants.

Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies

“…Vaccinium is the fifth genus of natural GMOs after Nicotiana , Linaria , Ipomoea, and Camellia , where the cT-DNA structure was characterized in greater detail in many species. [ 11 , 13 , 14 , 23 ].…”

“…An important feature of the work carried out by us was the use of a large number of forms of cranberries, lingonberries, and blueberries of different geographical origin, as well as the phasing of natural transgene alleles using SRA data in order to assess intraspecific variability. Such an approach was first used to study cellular T-DNA of representatives of the Camellia genus [ 23 ]. The analysis of individual alleles in phylogenetic studies makes it possible to identify acts of hybridization, including interspecific hybridization.…”

“…These discoveries enabled making a number of generalizations regarding the distribution, structures, and possible functions of cT-DNA, summarized in our previous paper [ 19 ]. Sequences of cT-DNAs have been used in phylogenetic studies of Linaria [ 20 ], Ipomoea [ 21 ], Nicotiana [ 22 ], and Camellia [ 23 ]. They present several advantages for exploring the origin and evolution of nGMO species.…”

“…This prevents the generation of multiple paralogs, which is a significant advantage over classical nuclear markers. Additionally, cT-DNAs can be large and old enough to generate a range of variants, thereby allowing the construction of detailed trees [ 23 ]. Phasing of T-DNA alleles enables the reconstruction of more precise phylogenetic relationships and identification of hybridization events in the evolution of plant species [ 24 ].…”

“…Phasing of T-DNA alleles enables the reconstruction of more precise phylogenetic relationships and identification of hybridization events in the evolution of plant species [ 24 ]. These approaches have been successfully applied in the study of the genus Camellia [ 23 ].…”