Journal of Integrative Plant Biology, volume 65, issue 10, pages 2242-2261
Cas9‐targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants
Merkulov Pavel
1, 2
,
Gvaramiya Sofya
1
,
Dudnikov Maxim
1, 2
,
Komakhin Roman A
1
,
Omarov Murad
1
,
Kocheshkova Alina
1
,
Soloviev Alexander
1, 3, 4
,
Kirov Ilya
1, 2
3
All‐Russia Center for Plant Quarantine Ramenski 140150 Russia
|
Publication type: Journal Article
Publication date: 2023-09-13
Journal:
Journal of Integrative Plant Biology
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 11.4
ISSN: 16729072, 17447909
Biochemistry
General Biochemistry, Genetics and Molecular Biology
Plant Science
Abstract
ABSTRACT
Transposable element insertions (TEIs) are an important source of genomic innovation by contributing to plant adaptation, speciation, and the production of new varieties. The often large, complex plant genomes make identifying TEIs from short reads difficult and expensive. Moreover, rare somatic insertions that reflect mobilome dynamics are difficult to track using short reads. To address these challenges, we combined Cas9‐targeted Nanopore sequencing (CANS) with the novel pipeline NanoCasTE to trace both genetically inherited and somatic TEIs in plants. We performed CANS of the EVADÉ (EVD) retrotransposon in wild‐type Arabidopsis thaliana and rapidly obtained up to 40x sequence coverage. Analysis of hemizygous T‐DNA insertion sites and genetically inherited insertions of the EVD transposon in the ddm1 genome uncovered the crucial role of DNA methylation in shaping EVD insertion preference. We also investigated somatic transposition events of the ONSEN transposon family, finding that genes that are downregulated during heat stress are preferentially targeted by ONSENs. Finally, we detected hypomethylation of novel somatic insertions for two ONSENs. CANS and NanoCasTE are effective tools for detecting TEIs and exploring mobilome organization in plants in response to stress and in different genetic backgrounds, as well as screening T‐DNA insertion mutants and transgenic plants.
This article is protected by copyright. All rights reserved.
Citations by journals
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International Journal of Molecular Sciences
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International Journal of Molecular Sciences
2 publications, 100%
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Citations by publishers
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Multidisciplinary Digital Publishing Institute (MDPI)
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Multidisciplinary Digital Publishing Institute (MDPI)
2 publications, 100%
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2
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Merkulov P. et al. Cas9‐targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants // Journal of Integrative Plant Biology. 2023. Vol. 65. No. 10. pp. 2242-2261.
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Merkulov P., Gvaramiya S., Dudnikov M., Komakhin R. A., Omarov M., Kocheshkova A., Konstantinov Z., Soloviev A., Karlov G. I., Divashuk M. G., Kirov I. Cas9‐targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants // Journal of Integrative Plant Biology. 2023. Vol. 65. No. 10. pp. 2242-2261.
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TY - JOUR
DO - 10.1111/jipb.13555
UR - https://doi.org/10.1111%2Fjipb.13555
TI - Cas9‐targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants
T2 - Journal of Integrative Plant Biology
AU - Merkulov, Pavel
AU - Gvaramiya, Sofya
AU - Dudnikov, Maxim
AU - Komakhin, Roman A
AU - Omarov, Murad
AU - Kocheshkova, Alina
AU - Konstantinov, Zakhar
AU - Soloviev, Alexander
AU - Karlov, Gennady I.
AU - Divashuk, Mikhail G.
AU - Kirov, Ilya
PY - 2023
DA - 2023/09/13 00:00:00
PB - Wiley
SP - 2242-2261
IS - 10
VL - 65
SN - 1672-9072
SN - 1744-7909
ER -
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@article{2023_Merkulov,
author = {Pavel Merkulov and Sofya Gvaramiya and Maxim Dudnikov and Roman A Komakhin and Murad Omarov and Alina Kocheshkova and Zakhar Konstantinov and Alexander Soloviev and Gennady I. Karlov and Mikhail G. Divashuk and Ilya Kirov},
title = {Cas9‐targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants},
journal = {Journal of Integrative Plant Biology},
year = {2023},
volume = {65},
publisher = {Wiley},
month = {sep},
url = {https://doi.org/10.1111%2Fjipb.13555},
number = {10},
pages = {2242--2261},
doi = {10.1111/jipb.13555}
}
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Merkulov, Pavel, et al. “Cas9‐targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants.” Journal of Integrative Plant Biology, vol. 65, no. 10, Sep. 2023, pp. 2242-2261. https://doi.org/10.1111%2Fjipb.13555.