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Molecular genetic and bioinformatic approaches for the allele reconstruction of the rolB/C-like gene in representatives of the genus Vaccinium L.
- Authors: Zhidkin R.R.1, Zhurbenko P.M.1,2, Gorodilova E.Y.1, Matveeva T.V.1
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Affiliations:
- Saint Petersburg State University
- Komarov Botanical Institute of the Russian Academy of Sciences
- Issue: Vol 20 (2022): Supplement
- Pages: 36-37
- Section: Genetically modified organism. The Нistory, Achivements, Social and Environmental Riscs
- Submitted: 03.11.2022
- Accepted: 11.11.2022
- Published: 08.12.2022
- URL: https://journals.eco-vector.com/ecolgenet/article/view/112368
- DOI: https://doi.org/10.17816/ecogen112368
- ID: 112368
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Abstract
Agrobacterium mediated transformation is one of the most studied examples of horizontal gene transfer between pro- and eukaryotes. During this process a part of the Ti-plasmid — T-DNA — is transferred into the plant cell genome. These sequences could be preserved in the genomes during evolution and inherited in a series of sexual generations. Such plants are described within the genus Vaccinium L. [1]. Our research team is currently analyzing natural transgenes in V. oxycoccos L., V. japonicum Miq., V. conchophyllum Rehder, V. emarginatum Hayata, V. myrtilloides Michx., V. virgatum Ait., V. corymbosum L., V. darrowii Camp, V. smallii A. Gray, V. praestans Lamb., V. ovalifolium Sm., V. myrtillus L., V. uliginosum L., V. vitis-idaea L.
Previously, analyzing the natural transgenes in another genus (Camellia L.) [2], we showed the importance of reconstructing the allelic states of transgenes for phylogenetic studies.
In this paper, we present a comprehensive approach for studying the allelic state of the rolB/C-like gene in plants of the genus Vaccinium. It combines molecular genetic and bioinformatic research methods.
Molecular genetic methods involve Sanger sequencing of a gene sequence in a large number of samples, while for each sample the sequence is presented as a set of polymorphic positions in binary form. Allele resolution occurs based on the description of alleles in homozygotes and a series of “subtractions” of known alleles in heterozygous samples. The second method involves the analysis of SRA (Sequence Read Archive) sequences available in the databases. SRA is a repository of high-throughput sequencing raw data.
Based on our work, we can conclude that both of these approaches make it possible to describe the allelic state of the rolB/C-like gene in representatives of the genus Vaccinium.
The work was performed using the equipment of the Resource Center of Saint Petersburg State University “Development of Molecular and Cellular Technologies” with the support of the Ministry of Science and Higher Education of the Russian Federation in accordance with agreement No. 075-15-2022-322 dated 04/22/2022 on the provision of a grant in the form of a subsidy from the Federal budget of the Russian Federation. The grant was provided as part of the state support for the creation and development of the world-class Scientific Center “Agrotechnologies for the Future”.
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Agrobacterium mediated transformation is one of the most studied examples of horizontal gene transfer between pro- and eukaryotes. During this process a part of the Ti-plasmid — T-DNA — is transferred into the plant cell genome. These sequences could be preserved in the genomes during evolution and inherited in a series of sexual generations. Such plants are described within the genus Vaccinium L. [1]. Our research team is currently analyzing natural transgenes in V. oxycoccos L., V. japonicum Miq., V. conchophyllum Rehder, V. emarginatum Hayata, V. myrtilloides Michx., V. virgatum Ait., V. corymbosum L., V. darrowii Camp, V. smallii A. Gray, V. praestans Lamb., V. ovalifolium Sm., V. myrtillus L., V. uliginosum L., V. vitis-idaea L.
Previously, analyzing the natural transgenes in another genus (Camellia L.) [2], we showed the importance of reconstructing the allelic states of transgenes for phylogenetic studies.
In this paper, we present a comprehensive approach for studying the allelic state of the rolB/C-like gene in plants of the genus Vaccinium. It combines molecular genetic and bioinformatic research methods.
Molecular genetic methods involve Sanger sequencing of a gene sequence in a large number of samples, while for each sample the sequence is presented as a set of polymorphic positions in binary form. Allele resolution occurs based on the description of alleles in homozygotes and a series of “subtractions” of known alleles in heterozygous samples. The second method involves the analysis of SRA (Sequence Read Archive) sequences available in the databases. SRA is a repository of high-throughput sequencing raw data.
Based on our work, we can conclude that both of these approaches make it possible to describe the allelic state of the rolB/C-like gene in representatives of the genus Vaccinium.
The work was performed using the equipment of the Resource Center of Saint Petersburg State University “Development of Molecular and Cellular Technologies” with the support of the Ministry of Science and Higher Education of the Russian Federation in accordance with agreement No. 075-15-2022-322 dated 04/22/2022 on the provision of a grant in the form of a subsidy from the Federal budget of the Russian Federation. The grant was provided as part of the state support for the creation and development of the world-class Scientific Center “Agrotechnologies for the Future”.
About the authors
Roman R. Zhidkin
Saint Petersburg State University
Email: st085586@student.spbu.ru
Graduate Student
Russian Federation, Saint PetersburgPeter M. Zhurbenko
Saint Petersburg State University; Komarov Botanical Institute of the Russian Academy of Sciences
Email: pj_28@mail.ru
Researcher, Laboratory of Biosystematics and Cytology, Junior Researcher, Department of Genetics and Biotechnology
Russian Federation, Saint Petersburg; Saint PetersburgElizabeth Yu. Gorodilova
Saint Petersburg State University
Email: elizaveta.gorodilova@spbu.ru
Sequencing Specialist, Resource Center of Saint Petersburg State University “Development of Molecular and Cellular Technologies”
Russian Federation, Saint PetersburgTatiana V. Matveeva
Saint Petersburg State University
Author for correspondence.
Email: radishlet@gmail.com
SPIN-code: 3877-6598
Dr. Sci. (Biol.), Professor
Russian Federation, Saint PetersburgReferences
- Matveeva TV. New naturally transgenic plants: 2020 update. Biol Commun. 2021;66(1): 36–46. doi: 10.21638/spbu03.2021.105
- Zhurbenko P, Klimenko F. Phase All: a simple tool for read-based allele phasing. Ecological Genetics. 2022;(In Press). (In Russ.)
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