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

A variety of plant species found in nature contain agrobacterial T-DNAs in their genomes which they transmit in a series of sexual generations. Such T-DNAs are called cellular T-DNAs (cT-DNAs). cT-DNAs have been discovered in dozens of plant genera, and are suggested to be used in phylogenetic studi...

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Autores principales: Zhidkin, Roman, Zhurbenko, Peter, Bogomaz, Olesya, Gorodilova, Elizaveta, Katsapov, Ivan, Antropov, Dmitry, Matveeva, Tatiana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10138537/
https://www.ncbi.nlm.nih.gov/pubmed/37108096
http://dx.doi.org/10.3390/ijms24086932
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author Zhidkin, Roman
Zhurbenko, Peter
Bogomaz, Olesya
Gorodilova, Elizaveta
Katsapov, Ivan
Antropov, Dmitry
Matveeva, Tatiana
author_facet Zhidkin, Roman
Zhurbenko, Peter
Bogomaz, Olesya
Gorodilova, Elizaveta
Katsapov, Ivan
Antropov, Dmitry
Matveeva, Tatiana
author_sort Zhidkin, Roman
collection PubMed
description A variety of plant species found in nature contain agrobacterial T-DNAs in their genomes which they transmit in a series of sexual generations. Such T-DNAs are called cellular T-DNAs (cT-DNAs). cT-DNAs have been discovered in dozens of plant genera, and are suggested to be used in phylogenetic studies, since they are well-defined and unrelated to other plant sequences. Their integration into a particular chromosomal site indicates a founder event and a clear start of a new clade. cT-DNA inserts do not disseminate in the genome after insertion. They can be large and old enough to generate a range of variants, thereby allowing the construction of detailed trees. Unusual cT-DNAs (containing the rolB/C-like gene) were found in our previous study in the genome data of two Vaccinium L. species. Here, we present a deeper study of these sequences in Vaccinium L. Molecular-genetic and bioinformatics methods were applied for sequencing, assembly, and analysis of the rolB/C-like gene. The rolB/C-like gene was discovered in 26 new Vaccinium species and Agapetes serpens (Wight) Sleumer. Most samples were found to contain full-size genes. It allowed us to develop approaches for the phasing of cT-DNA alleles and reconstruct a Vaccinium phylogenetic relationship. Intra- and interspecific polymorphism found in cT-DNA makes it possible to use it for phylogenetic and phylogeographic studies of the Vaccinium genus.
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spelling pubmed-101385372023-04-28 Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies Zhidkin, Roman Zhurbenko, Peter Bogomaz, Olesya Gorodilova, Elizaveta Katsapov, Ivan Antropov, Dmitry Matveeva, Tatiana Int J Mol Sci Article A variety of plant species found in nature contain agrobacterial T-DNAs in their genomes which they transmit in a series of sexual generations. Such T-DNAs are called cellular T-DNAs (cT-DNAs). cT-DNAs have been discovered in dozens of plant genera, and are suggested to be used in phylogenetic studies, since they are well-defined and unrelated to other plant sequences. Their integration into a particular chromosomal site indicates a founder event and a clear start of a new clade. cT-DNA inserts do not disseminate in the genome after insertion. They can be large and old enough to generate a range of variants, thereby allowing the construction of detailed trees. Unusual cT-DNAs (containing the rolB/C-like gene) were found in our previous study in the genome data of two Vaccinium L. species. Here, we present a deeper study of these sequences in Vaccinium L. Molecular-genetic and bioinformatics methods were applied for sequencing, assembly, and analysis of the rolB/C-like gene. The rolB/C-like gene was discovered in 26 new Vaccinium species and Agapetes serpens (Wight) Sleumer. Most samples were found to contain full-size genes. It allowed us to develop approaches for the phasing of cT-DNA alleles and reconstruct a Vaccinium phylogenetic relationship. Intra- and interspecific polymorphism found in cT-DNA makes it possible to use it for phylogenetic and phylogeographic studies of the Vaccinium genus. MDPI 2023-04-08 /pmc/articles/PMC10138537/ /pubmed/37108096 http://dx.doi.org/10.3390/ijms24086932 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhidkin, Roman
Zhurbenko, Peter
Bogomaz, Olesya
Gorodilova, Elizaveta
Katsapov, Ivan
Antropov, Dmitry
Matveeva, Tatiana
Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies
title Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies
title_full Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies
title_fullStr Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies
title_full_unstemmed Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies
title_short Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies
title_sort biodiversity of rolb/c-like natural transgene in the genus vaccinium l. and its application for phylogenetic studies
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10138537/
https://www.ncbi.nlm.nih.gov/pubmed/37108096
http://dx.doi.org/10.3390/ijms24086932
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