Evolution of DNA methylome diversity in eukaryotes

A de Mendoza, R Lister, O Bogdanovic - Journal of Molecular Biology, 2020 - Elsevier
Cytosine DNA methylation (5mC) is a widespread base modification in eukaryotic genomes
with critical roles in transcriptional regulation. In recent years, our understanding of 5mC has …

Phylogenetics is the new genetics (for most of biodiversity)

SD Smith, MW Pennell, CW Dunn… - Trends in Ecology & …, 2020 - cell.com
Despite substantial progress in understanding the genetic basis for differences in
morphology, physiology, and behavior, many phenotypes of interest are difficult to study with …

Molecular properties of epimutation hotspots

RR Hazarika, M Serra, Z Zhang, Y Zhang, RJ Schmitz… - Nature plants, 2022 - nature.com
Mistakes in the maintenance of CG methylation are a source of heritable epimutations in
plants. Multigenerational surveys indicate that the rate of these stochastic events varies …

Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation

Q Hu, Y Ma, T Mandáková, S Shi… - Proceedings of the …, 2021 - National Acad Sciences
Deserts exert strong selection pressures on plants, but the underlying genomic drivers of
ecological adaptation and subsequent speciation remain largely unknown. Here, we …

Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae

N Walden, DA German, EM Wolf, M Kiefer… - Nature …, 2020 - nature.com
Angiosperms have become the dominant terrestrial plant group by diversifying for~ 145
million years into a broad range of environments. During the course of evolution, numerous …

Inter-species association mapping links splice site evolution to METTL16 and SNRNP27K

MT Parker, SM Fica, GJ Barton, GG Simpson - Elife, 2023 - elifesciences.org
Eukaryotic genes are interrupted by introns that are removed from transcribed RNAs by
splicing. Patterns of splicing complexity differ between species, but it is unclear how these …

Stochasticity in gene body methylation

C Goeldel, F Johannes - Current Opinion in Plant Biology, 2023 - Elsevier
Gene body methylation (gbM) is a widely conserved epigenetic feature of plant genomes.
Efforts to delineate the mechanisms by which gbM contributes to transcriptional regulation …

Leaf shape diversity: from genetic modules to computational models

N Bhatia, A Runions, M Tsiantis - Annual Review of Plant …, 2021 - annualreviews.org
Plant leaves display considerable variation in shape. Here, we introduce key aspects of leaf
development, focusing on the morphogenetic basis of leaf shape diversity. We discuss the …

Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway

LC Wheeler, JF Walker, J Ng, R Deanna… - Molecular Biology …, 2022 - academic.oup.com
Dissecting the relationship between gene function and substitution rates is key to
understanding genome-wide patterns of molecular evolution. Biochemical pathways provide …

Heterochromatin is a quantitative trait associated with spontaneous epiallele formation

Y Zhang, H Jang, R Xiao, I Kakoulidou… - Nature …, 2021 - nature.com
Epialleles are meiotically heritable variations in expression states that are independent from
changes in DNA sequence. Although they are common in plant genomes, their molecular …