Description of new naturally transgenic plants enables estimation of the time intervals of horizontal gene transfer from agrobacterium to plants

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Abstract

BACKGROUND: Horizontal gene transfer from Agrobacterium to dicotyledonous plants leads to the emergence of naturally transgenic species containing DNA fragments known as cellular T-DNA. Such plants are also referred to as naturally genetically modified organisms (GMOs). The continuous expansion of nucleotide sequence databases and advances in bioinformatics methods have made it possible to systematically identify natural transgenes in deposited genomes of various dicot species, thereby expanding the list of known natural GMOs. Detailed investigation of horizontally transferred sequences opens opportunities for their comparative analysis.

AIM: To search for and analyze sequences homologous to Agrobacterium T-DNA in the genomes of dicotyledonous plants and subsequently estimate the timing of horizontal gene transfer events based on comparisons of extended inverted repeats of cellular T-DNA.

METHODS: Data from the WGS and TSA nucleotide sequence databases were used, together with BLAST alignment algorithms.

RESULTS: A total of 93 new species of naturally transgenic plants were identified. Based on the analysis of cellular T-DNA sequences present as inverted repeats, approximate timing of horizontal gene transfer events was estimated for 28 species of natural GMOs. The analysis revealed numerous common features in the evolution of transgenes between the newly identified natural GMOs and other examples of horizontal gene transfer. It was established that the transfer events occurred between 0.62 and 24 million years ago, spanning three periods of the Cenozoic era.

CONCLUSION: The obtained results may be used to investigate the evolutionary role of cellular T-DNA and horizontal gene transfer in naturally transgenic plants.

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About the authors

Anton D. Shaposhnikov

Saint Petersburg State University

Author for correspondence.
Email: st096319@student.spbu.ru
ORCID iD: 0009-0002-7905-2999
SPIN-code: 5145-8352
Russian Federation, Saint Petersburg

Tatiana V. Matveeva

Saint Petersburg State University; All-Russian Research Institute of Plant Protection

Email: radishlet@gmail.com
ORCID iD: 0000-0001-8569-6665
SPIN-code: 3877-6598

Dr. Sci. (Biology), Professor

Russian Federation, Saint Petersburg; Saint Petersburg

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Supplementary files

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2. Supplement 1. cT-DNA found in WGS and TSA database.xlsx
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3. Fig. 1. Diagram showing the ratio of the number of natural GMOs to the total number of deposited genomes of dicotyledonous plants.

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4. Fig. 2. Number of natural GMO species with different types of cellular T-DNA.

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5. Fig. 3. Distribution of intact and non-intact natural transgenes among the three types of cellular T-DNA identified in WGS data: a, cellular T-DNA containing opine synthase genes and oncogenes; b, cellular T-DNA containing only opine synthase genes; c, cellular T-DNA containing only oncogenes. Intact sequences are indicated by “+”, whereas non-intact sequences are indicated by “–”.

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6. Fig. 4. Diagram showing the estimated timing of horizontal gene transfer events represented by inverted repeats of cellular T-DNA in natural GMOs.

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