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Plants, volume 11, issue 24, pages 3579

Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower (Helianthus annuus L.) Revealed the Origin of the Plant Retrotranscriptome

Kirov Ilya ^{1, 2}

Merkulov Pavel ^{1, 2}

Polkhovskaya Ekaterina ²

Konstantinov Zakhar ²

Kazancev Mikhail ^{1, 2}

Saenko Ksenia ^{2, 3}

Polkhovskiy Alexander ^{1, 2, 4}

Dudnikov Maxim ^{1, 2}

Garibyan Tsovinar ²

Demurin Yakov ⁵

Soloviev Alexander ²

Hide authors affiliations Show authors affiliations: 5 affiliations

Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia |

All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia |

Federal Research Center of Biological Plant Protection, 350039 Krasnodar, Russia |

⁴

Skolkovo Institute of Science and Technology, 121205 Moscow, Russia |

⁵

Pustovoit All-Russia Research Institute of Oilseed Crops, Filatova St. 17, 350038 Krasnodar, Russia |

Publication type: Journal Article

Publication date: 2022-12-19

Multidisciplinary Digital Publishing Institute (MDPI)

Journal: Plants

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Quartile WOS

Impact factor: 4.5

ISSN: 22237747

DOI: 10.3390/plants11243579

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Plant Science

Ecology, Evolution, Behavior and Systematics

Ecology

Abstract

Transposable elements (TEs) contribute not only to genome diversity but also to transcriptome diversity in plants. To unravel the sources of LTR retrotransposon (RTE) transcripts in sunflower, we exploited a recently developed transposon activation method (‘TEgenesis’) along with long-read cDNA Nanopore sequencing. This approach allows for the identification of 56 RTE transcripts from different genomic loci including full-length and non-autonomous RTEs. Using the mobilome analysis, we provided a new set of expressed and transpositional active sunflower RTEs for future studies. Among them, a Ty3/Gypsy RTE called SUNTY3 exhibited ongoing transposition activity, as detected by eccDNA analysis. We showed that the sunflower genome contains a diverse set of non-autonomous RTEs encoding a single RTE protein, including the previously described TR-GAG (terminal repeat with the GAG domain) as well as new categories, TR-RT-RH, TR-RH, and TR-INT-RT. Our results demonstrate that 40% of the loci for RTE-related transcripts (nonLTR-RTEs) lack their LTR sequences and resemble conventional eucaryotic genes encoding RTE-related proteins with unknown functions. It was evident based on phylogenetic analysis that three nonLTR-RTEs encode GAG (HadGAG1-3) fused to a host protein. These HadGAG proteins have homologs found in other plant species, potentially indicating GAG domestication. Ultimately, we found that the sunflower retrotranscriptome originated from the transcription of active RTEs, non-autonomous RTEs, and gene-like RTE transcripts, including those encoding domesticated proteins.

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Plants	Plants, 1, 50% Plants 1 publication, 50%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 1, 50% International Journal of Molecular Sciences 1 publication, 50%
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Kirov I. et al. Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower (Helianthus annuus L.) Revealed the Origin of the Plant Retrotranscriptome // Plants. 2022. Vol. 11. No. 24. p. 3579.

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Kirov I., Merkulov P., Polkhovskaya E., Konstantinov Z., Kazancev M., Saenko K., Polkhovskiy A., Dudnikov M., Garibyan T., Demurin Y., Soloviev A. Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower (Helianthus annuus L.) Revealed the Origin of the Plant Retrotranscriptome // Plants. 2022. Vol. 11. No. 24. p. 3579.

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TY - JOUR

DO - 10.3390/plants11243579

UR - https://doi.org/10.3390%2Fplants11243579

TI - Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower (Helianthus annuus L.) Revealed the Origin of the Plant Retrotranscriptome

T2 - Plants

AU - Kirov, Ilya

AU - Merkulov, Pavel

AU - Polkhovskaya, Ekaterina

AU - Konstantinov, Zakhar

AU - Kazancev, Mikhail

AU - Saenko, Ksenia

AU - Polkhovskiy, Alexander

AU - Dudnikov, Maxim

AU - Garibyan, Tsovinar

AU - Demurin, Yakov

AU - Soloviev, Alexander

PY - 2022

DA - 2022/12/19 00:00:00

PB - Multidisciplinary Digital Publishing Institute (MDPI)

SP - 3579

IS - 24

VL - 11

SN - 2223-7747

ER -

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@article{2022_Kirov,

author = {Ilya Kirov and Pavel Merkulov and Ekaterina Polkhovskaya and Zakhar Konstantinov and Mikhail Kazancev and Ksenia Saenko and Alexander Polkhovskiy and Maxim Dudnikov and Tsovinar Garibyan and Yakov Demurin and Alexander Soloviev},

title = {Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower (Helianthus annuus L.) Revealed the Origin of the Plant Retrotranscriptome},

journal = {Plants},

year = {2022},

volume = {11},

publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},

month = {dec},

url = {https://doi.org/10.3390%2Fplants11243579},

number = {24},

pages = {3579},

doi = {10.3390/plants11243579}

}

MLA

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Kirov, Ilya, et al. “Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower (Helianthus annuus L.) Revealed the Origin of the Plant Retrotranscriptome.” Plants, vol. 11, no. 24, Dec. 2022, p. 3579. https://doi.org/10.3390%2Fplants11243579.

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Publisher

Multidisciplinary Digital Publishing Institute (MDPI)

Journal

Plants

Quartile SCImago

Quartile WOS

Impact factor

4.5

ISSN

22237747 (Electronic)

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