Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis

G Del Toro-De León, J van Boven… - Nucleic Acids …, 2024 - academic.oup.com
Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene
expression, has independently evolved in the endosperm of flowering plants and the …

A review of strategies used to identify transposition events in plant genomes

M Bajus, A Macko-Podgórni, D Grzebelus… - Frontiers in Plant …, 2022 - frontiersin.org
Transposable elements (TEs) were initially considered redundant and dubbed 'junk DNA'.
However, more recently they were recognized as an essential element of genome plasticity …

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

P Merkulov, E Egorova, I Kirov - Plants, 2023 - mdpi.com
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 …

Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line

S Han, GB Dias, PJ Basting, R Viswanatha… - Nucleic acids …, 2022 - academic.oup.com
Animal cell lines often undergo extreme genome restructuring events, including polyploidy
and segmental aneuploidy that can impede de novo whole-genome assembly (WGA). In …

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

I Kirov, P Merkulov, E Polkhovskaya, Z Konstantinov… - Plants, 2022 - mdpi.com
Transposable elements (TEs) contribute not only to genome diversity but also to
transcriptome diversity in plants. To unravel the sources of LTR retrotransposon (RTE) …

Genome assembly, annotation and evolutionary insights from the draft genome of wild pomegranate

R Mahajan, S Gupta, N Tanoj, T Sagar, S Kaur… - Protoplasma, 2024 - Springer
Wild pomegranate is a potent medicinal plant known for its medicinal and nutritional
attributes. Despite its healing and curative properties, the genome of this wild species …

Illuminating the plant transposon insertion landscape in real time using Cas9-targeted Nanopore sequencing and a novel pipeline

I Kirov, P Merkulov, S Gvaramiya, R Komakhin… - BioRxiv, 2021 - biorxiv.org
Transposable elements (TEs) are a major source of genomic novelty, contributing to plant
adaptation, speciation and new cultivar production. The often large, complex genomes of …

Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm

G del Toro-de León, J van Boven, J Santos-González… - bioRxiv, 2024 - biorxiv.org
Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene
expression, has independently evolved in the endosperm of flowering plants and the …

Cas9‐targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants

P Merkulov, S Gvaramiya, M Dudnikov… - Journal of Integrative …, 2023 - Wiley Online Library
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 …

[HTML][HTML] Ongoing endeavors to detect mobilization of transposable elements

Y Lee, U Ha, S Moon - BMB reports, 2022 - ncbi.nlm.nih.gov
Transposable elements (TEs) are DNA sequences capable of mobilization from one location
to another in the genome. Since the discovery of 'Dissociation (Dc) locus' by Barbara …