The epigenetic control of the transposable element life cycle in plant genomes and beyond

P Liu, D Cuerda-Gil, S Shahid… - Annual Review of …, 2022 - annualreviews.org
Within the life cycle of a living organism, another life cycle exists for the selfish genome
inhabitants, which are called transposable elements (TEs). These mobile sequences invade …

Molecular mechanisms of adaptive evolution in wild animals and plants

Y Hu, X Wang, Y Xu, H Yang, Z Tong, R Tian… - Science China Life …, 2023 - Springer
Wild animals and plants have developed a variety of adaptive traits driven by adaptive
evolution, an important strategy for species survival and persistence. Uncovering the …

Major impacts of widespread structural variation on gene expression and crop improvement in tomato

M Alonge, X Wang, M Benoit, S Soyk, L Pereira… - Cell, 2020 - cell.com
Structural variants (SVs) underlie important crop improvement and domestication traits.
However, resolving the extent, diversity, and quantitative impact of SVs has been …

A pangenome analysis pipeline provides insights into functional gene identification in rice

J Wang, W Yang, S Zhang, H Hu, Y Yuan, J Dong… - Genome Biology, 2023 - Springer
Background A pangenome aims to capture the complete genetic diversity within a species
and reduce bias in genetic analysis inherent in using a single reference genome. However …

Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

P Baduel, B Leduque, A Ignace, I Gy, J Gil Jr, O Loudet… - Genome biology, 2021 - Springer
Background How species can adapt to abrupt environmental changes, particularly in the
absence of standing genetic variation, is poorly understood and a pressing question in the …

Epigenetics: a catalyst of plant immunity against pathogens

A Hannan Parker, SW Wilkinson, J Ton - New Phytologist, 2022 - Wiley Online Library
The plant immune system protects against pests and diseases. The recognition of stress‐
related molecular patterns triggers localised immune responses, which are often followed by …

[HTML][HTML] Integrating multi-omics data for crop improvement

F Scossa, S Alseekh, AR Fernie - Journal of plant physiology, 2021 - Elsevier
Our agricultural systems are now in urgent need to secure food for a growing world
population. To meet this challenge, we need a better characterization of plant genetic and …

Domestication of crop metabolomes: desired and unintended consequences

S Alseekh, F Scossa, W Wen, J Luo, J Yan… - Trends in Plant …, 2021 - cell.com
The majority of the crops and vegetables of today were domesticated from their wild
progenitors within the past 12 000 years. Considerable research effort has been expended …

How the pan-genome is changing crop genomics and improvement

R Della Coletta, Y Qiu, S Ou, MB Hufford, CN Hirsch - Genome biology, 2021 - Springer
Crop genomics has seen dramatic advances in recent years due to improvements in
sequencing technology, assembly methods, and computational resources. These advances …

The important contribution of transposable elements to phenotypic variation and evolution

NS Catlin, EB Josephs - Current opinion in plant biology, 2022 - Elsevier
Transposable elements (TEs) are responsible for significant genomic variation in plants. Our
understanding of the evolutionary forces shaping TE polymorphism has lagged behind other …