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

Kirov, Ilya; Merkulov, Pavel; Polkhovskaya, Ekaterina; Konstantinov, Zakhar; Kazancev, Mikhail; Saenko, Ksenia; Polkhovskiy, Alexander; Dudnikov, Maxim; Garibyan, Tsovinar; Demurin, Ya.N.; Soloviev, A. A.

doi:10.3390/plants11243579

Cited by 4 publications

(3 citation statements)

References 52 publications

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“…Previous investigations claimed that plants grown on ZA media and subjected to stress, such as heat stress, are stimulated to produce eccDNAs [10,17]. We combined epigenetic (ZA) stress with each of the following stimuli to detect stress-responsive eccDNA loci: heat stress (HS), flagellin treatment (Flg), and abscisic acid treatment (ABA).…”

Section: Detection Of Eccdnas Under Abiotic Hormone and Flagellin Tre...mentioning

confidence: 99%

Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing

Merkulov

Егорова

Kirov

2023

Plants

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Extrachromosomal circular DNAs (eccDNAs) are enigmatic DNA molecules that have been detected in a range of organisms. In plants, eccDNAs have various genomic origins and may be derived from transposable elements. The structures of individual eccDNA molecules and their dynamics in response to stress are poorly understood. In this study, we showed that nanopore sequencing is a useful tool for the detection and structural analysis of eccDNA molecules. Applying nanopore sequencing to the eccDNA molecules of epigenetically stressed Arabidopsis plants grown under various stress treatments (heat, abscisic acid, and flagellin), we showed that TE-derived eccDNA quantity and structure vary dramatically between individual TEs. Epigenetic stress alone did not cause eccDNA up-regulation, whereas its combination with heat stress triggered the generation of full-length and various truncated eccDNAs of the ONSEN element. We showed that the ratio between full-length and truncated eccDNAs is TE- and condition-dependent. Our work paves the way for further elucidation of the structural features of eccDNAs and their connections with various biological processes, such as eccDNA transcription and eccDNA-mediated TE silencing.

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Section: Detection Of Eccdnas Under Abiotic Hormone and Flagellin Tre...mentioning

confidence: 99%

Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing

Merkulov

Егорова

Kirov

2023

Plants

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“…However, the utilization of this method in other plant species has not been sufficiently demonstrated. Recently, TEgenesis was applied to reactivate TEs in sunflowers [55]. The authors demonstrated the induction of expression for 16 TE-related loci, and ten of them also showed copy number variation between sunflower varieties, indicating transposition potential.…”

Section: Controlled Activation Of Tes Via Polii and Dna Methylation I...mentioning

confidence: 99%

“…Before the broad creation and application of iTE collections, several obstacles must be resolved. First, the developed TEgenesis approaches seem to be very harmful for plants, reducing the plant survival rate [55]; therefore, alternative approaches need to be developed to ensure TEI occurrence in germline plant cells, enabling the genetic inheritance of novel TEIs. Second, the number of active TEs for which the triggering factor is known is extremely low.…”

Section: Challenges and Emerging Perspectives Of Te-mediated Biologic...mentioning

confidence: 99%

Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding

Kirov

2023

IJMS

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Genetic diversity is a key factor for plant breeding. The birth of novel genic and genomic variants is also crucial for plant adaptation in nature. Therefore, the genomes of almost all living organisms possess natural mutagenic mechanisms. Transposable elements (TEs) are a major mutagenic force driving genetic diversity in wild plants and modern crops. The relatively rare TE transposition activity during the thousand-year crop domestication process has led to the phenotypic diversity of many cultivated species. The utilization of TE mutagenesis by artificial and transient acceleration of their activity in a controlled mode is an attractive foundation for a novel type of mutagenesis called TE-mediated biological mutagenesis. Here, I focus on TEs as mutagenic sources for plant breeding and discuss existing and emerging transgene-free approaches for TE activation in plants. Furthermore, I also review the non-randomness of TE insertions in a plant genome and the molecular and epigenetic factors involved in shaping TE insertion preferences. Additionally, I discuss the molecular mechanisms that prevent TE transpositions in germline plant cells (e.g., meiocytes, pollen, egg and embryo cells, and shoot apical meristem), thereby reducing the chances of TE insertion inheritance. Knowledge of these mechanisms can expand the TE activation toolbox using novel gene targeting approaches. Finally, the challenges and future perspectives of plant populations with induced novel TE insertions (iTE plant collections) are discussed.

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Bioinformatics in Russia: history and present-day landscape

Nawaz,

Pamirsky,

Golokhvast

2024

Briefings in Bioinformatics

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Bioinformatics has become an interdisciplinary subject due to its universal role in molecular biology research. The current status of Russia’s bioinformatics research in Russia is not known. Here, we review the history of bioinformatics in Russia, present the current landscape, and highlight future directions and challenges. Bioinformatics research in Russia is driven by four major industries: information technology, pharmaceuticals, biotechnology, and agriculture. Over the past three decades, despite a delayed start, the field has gained momentum, especially in protein and nucleic acid research. Dedicated and shared centers for genomics, proteomics, and bioinformatics are active in different regions of Russia. Present-day bioinformatics in Russia is characterized by research issues related to genetics, metagenomics, OMICs, medical informatics, computational biology, environmental informatics, and structural bioinformatics. Notable developments are in the fields of software (tools, algorithms, and pipelines), use of high computation power (e.g. by the Siberian Supercomputer Center), and large-scale sequencing projects (the sequencing of 100 000 human genomes). Government funding is increasing, policies are being changed, and a National Genomic Information Database is being established. An increased focus on eukaryotic genome sequencing, the development of a common place for developers and researchers to share tools and data, and the use of biological modeling, machine learning, and biostatistics are key areas for future focus. Universities and research institutes have started to implement bioinformatics modules. A critical mass of bioinformaticians is essential to catch up with the global pace in the discipline.

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

Cited by 4 publications

References 52 publications

Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing

Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing

Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding

Bioinformatics in Russia: history and present-day landscape

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