Entries by Matthias Benoit

Slice and Dice: DCL2 Mediates the Production of 22-nt siRNAs That Influence Trait Variation in Soybean

In plants, small interfering RNAs (siRNAs) serve as key regulators of gene expression. While 24-nucleotide (nt) siRNAs are produced by DCL3 and mediate transcriptional silencing of transposons and pericentromeric chromatin through RdDM (Borges and Martienssen, 2015), 22-nt siRNAs are processed by DCL2 and participate in transgene silencing and viral defense (Wang et al., 2018; Parent […]

The Great Escape: How a Plant DNA Virus Hijacks an Imprinted Host Gene to Avoid Silencing

Plant viruses are a major threat to global food security. The large family of geminiviruses has a broad pathogenic impact on economically important crops such as maize, tomato, and cassava and causes millions of tons of losses per year worldwide (Rojas et al., 2005). Geminiviruses possess a circular DNA genome encoding proteins necessary for viral […]

In the Transcripts: Long-read Transcriptomics Enables a Novel Type of Transposable Element Annotation in Plants

Transposable Elements (TEs) are mobile genetic elements and major constituents of eukaryotic chromosomes. TEs promote genetic and epigenetic variation within genomes and are a major source of evolutionary novelty and adaptation (Lisch, 2013). In plants, TEs represent from 20% of the genomic content in Arabidopsis thaliana to 85% in maize (Zea mays). Structural characterization of […]

On the Importance of Variation: A High-Resolution Map of Copy Number Variants in Arabidopsis

Linking genotype to phenotype is a major challenge in plant biology. Phenotypic variation observed between individuals of a same plant species is the consequence of a vast array of genetic variation, including Single Nucleotide Polymorphisms (SNPs) and small or large structural variants including Copy Number Variation (CNV). CNVs are genetic polymorphisms in which a segment […]

Heritable phenotypic variation due to partial maintenance of organ-specific epigenetic marks during asexual reproduction ($) (PNAS)

Clonal propagation is widely used by humans to maintain and propagate desirable phenotypic traits in plants. Despite a restricted genetic variety, phenotypical difference, known a somaclonal variation, arises sometimes between parents and the clonally propagated progeny. Some of this variability is attributed to epigenetic variation, but the origins and underlying molecular principles remain unclear. By […]

Tea genome expansion linked to TE bursts (Plant Biotechnol. J.)

Expansion of plant genomes is thought to be linked to massive bursts of transposable elements activity. This implies consequences on the distribution of epigenetic modifications required for the silencing of the causative transposons. Consequences of transposon bursts have been extensively described in compact plant genomes such as Arabidopsis or rice, but similar analyses in very […]

Postzygotic reproductive isolation via sequestration of a transposon-derived siRNA ($) (Devel. Cell)

Hybridization of plants with distinct chromosome number often results in seed development defects due to a phenomenon known as the triploid block. While this is triggered by the unbalanced expression of some paternally and maternally imprinted alleles, the molecular basis of the triploid block is not fully understood. The authors describe here that the paternally […]

Stony hard phenotype in peach due to transposon insertion into YUCCA ($) (Plant J)

Fruit softening in melting-flesh peaches is triggered by a major accumulation of ethylene at the late stage of ripening. Existence of stony hard peaches showing inhibition of fruit softening has been correlated with low levels of indole-3-acetic-acid inducing low levels of ethylene, but the underlying molecular cause remains unknown. Using ultra-performance liquid chromatography and tandem […]

DNA methylation footprints during soybean domestication and improvement (Genome Biol)

Crop domestication relies on harnessing the natural genomic diversity present in the cultivated population. The contribution of genetic variation for selection and improvement of traits in plants has been extensively studied. Besides this, variation in epigenetic components such as DNA methylation offers an alternative and mostly independent source of variability, but the contribution of epigenetic […]