Description of new naturally transgenic plants and estimation of time intervals of horizontal gene transfer events from agrobacteria to plants



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Abstract

BACKGROUND: Horizontal gene transfer from agrobacteria to dicotyledonous plants leads to the emergence of naturally transgenic species containing DNA fragments known as cellular T-DNA (cT-DNA). Such plants are also referred to as natural GMOs (nGMOs). The continuous expansion of nucleotide databases and the development of bioinformatic methods have enabled the systematic identification of natural transgenes in the deposited genomes of various dicot species, expanding the list of known nGMOs. Detailed investigation of the horizontally transferred sequences opens up opportunities for their comparative analysis.

AIM: The aim of this work was to search for and analyze sequences homologous to Agrobacterium T-DNA in the genomes of dicotyledonous plants, and to subsequently determine the timing of horizontal gene transfer events based on a comparison of extended inverted repeats of cT-DNA.

METHODS: The work used data from the WGS and TSA nucleotide sequence databases, as well as BLAST alignment algorithms.

RESULTS: As a result, 93 new species of naturally transgenic plants were discovered. Based on the analysis of cT-DNA presented as inverted repeats, the approximate timing of horizontal gene transfer events was estimated for 28 nGMO species. The conducted analysis revealed many common features in the evolution of transgenes between the nGMOs we discovered and other examples of horizontal gene transfer. It was established that the transfer events occurred in the period from 0.62 to 24 million years ago, which spans three periods of the Cenozoic era.

CONCLUSION: The discovery of new naturally transgenic plant species expands our understanding of the prevalence of horizontal gene transfer from agrobacteria to dicotyledonous plants and the evolutionary role of cT-DNA, while also providing material for further research and comparison with other cases of horizontal gene transfer. Dating the events of horizontal gene transfer makes it possible to estimate the time frame of this process in the evolution of naturally transgenic plants.

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About the authors

Anton D. Shaposhnikov

St. Petersburg State University

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

junior researcher

Russian Federation, 7–9 Universitetskaya emb., Saint Petersburg, 199034, Russian Federation;

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
Scopus Author ID: 7006494611

Dr. Sci. (Biology), Professor, department of genetics and biotechnology

Russian Federation, 7–9 Universitetskaya emb., Saint Petersburg, 199034, Russian Federation; Podbelskogo, 3, St.Petersburg – Pushkin, 196608, Russian Federation

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