Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

DR Agius, A Kapazoglou, E Avramidou… - Frontiers in Plant …, 2023 - frontiersin.org
Epigenetic modifications play a vital role in the preservation of genome integrity and in the
regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic …

Isoform sequencing and state-of-art applications for unravelling complexity of plant transcriptomes

D An, HX Cao, C Li, K Humbeck, W Wang - Genes, 2018 - mdpi.com
Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-
generation sequencing (TGS), offers longer reads than the second-generation sequencing …

Computational methods and next-generation sequencing approaches to analyze epigenetics data: profiling of methods and applications

I Arora, TO Tollefsbol - Methods, 2021 - Elsevier
Epigenetics is mainly comprised of features that regulate genomic interactions thereby
playing a crucial role in a vast array of biological processes. Epigenetic mechanisms such …

Plant DNA methylation responds to nutrient stress

X Fan, L Peng, Y Zhang - Genes, 2022 - mdpi.com
Nutrient stress as abiotic stress has become one of the important factors restricting crop yield
and quality. DNA methylation is an essential epigenetic modification that can effectively …

Zebularine treatment is associated with deletion of FTB1 leading to an increase in spikelet number in bread wheat

EJ Finnegan, B Ford, X Wallace… - Plant, cell & …, 2018 - Wiley Online Library
The number of rachis nodes (spikelets) on a wheat spike is a component of grain yield that
correlates with flowering time. The genetic basis regulating flowering in cereals is well …

A cost reduced variant of epi-genotyping by sequencing for studying DNA methylation in non-model organisms

O Werner, ÁS Prudencio… - Frontiers in Plant …, 2020 - frontiersin.org
Reference-free reduced representation bisulfite sequencing uses enzymatic digestion for
reducing genome complexity and allows detection of markers to study DNA methylation of a …

DNA methylation analysis in plants: review of computational tools and future perspectives

J Omony, T Nussbaumer, R Gutzat - Briefings in bioinformatics, 2020 - academic.oup.com
Genome-wide DNA methylation studies have quickly expanded due to advances in next-
generation sequencing techniques along with a wealth of computational tools to analyze the …

Rice Pangenome Genotyping Array: an efficient genotyping solution for pangenome‐based accelerated genetic improvement in rice

A Daware, A Malik, R Srivastava, D Das… - The Plant …, 2023 - Wiley Online Library
The advent of the pangenome era has unraveled previously unknown genetic variation
existing within diverse crop plants, including rice. This untapped genetic variation is …

Long-term methylome changes after experimental seed demethylation and their interaction with recurrent water stress in Erodium cicutarium (Geraniaceae)

F Balao, M Medrano, P Bazaga, O Paun, C Alonso - bioRxiv, 2023 - biorxiv.org
The frequency and length of drought periods are increasing in subtropical and temperate
regions worldwide. Epigenetic responses to water stress could be key for plant resilience to …

Riluzole administration to rats with levodopa-induced dyskinesia leads to loss of DNA methylation in neuronal genes

L Pagliaroli, A Fothi, E Nespoli, I Liko, B Veto, P Devay… - Cells, 2021 - mdpi.com
Dyskinesias are characterized by abnormal repetitive involuntary movements due to
dysfunctional neuronal activity. Although levodopa-induced dyskinesia, characterized by tic …