Epigenetic Variability Among Saffron Crocus ( L.) Accessions Characterized by Different Phenotypes.

This work represents the first epigenomic study carried out on saffron crocus. Five accessions of saffron, showing differences in tepal pigmentation, yield of saffron and flowering time, were analyzed at the epigenetic level by applying a methylation-sensitive restriction enzyme-sequencing (MRE-seq) approach. Five accession-specific hypomethylomes plus a reference hypomethylome, generated by combining the sequence data from the single accessions, were obtained.

Elucidating Drought Stress Tolerance in European Oaks Through Cross-Species Transcriptomics.

The impact of climate change that comes with a dramatic increase of long periods of extreme summer drought associated with heat is a fundamental challenge for European forests. As a result, forests are expected to shift their distribution patterns toward north-east, which may lead to a dramatic loss in value of European forest land. Consequently, unraveling key processes that underlie drought stress tolerance is not only of great scientific but also of utmost economic importance for forests to withstand future heat and drought wave scenarios.

YPR2 is a regulator of light modulated carbon and secondary metabolism in Trichoderma reesei.

Background: Filamentous fungi have evolved to succeed in nature by efficient growth and degradation of substrates, but also due to the production of secondary metabolites including mycotoxins. For Trichoderma reesei, as a biotechnological workhorse for homologous and heterologous protein production, secondary metabolite secretion is of particular importance for industrial application. Recent studies revealed an interconnected regulation of enzyme gene expression and carbon metabolism with secondary metabolism.

Identification and characterization of the Fasciola hepatica sodium- and chloride-dependent taurine transporter.

The parasitic liver fluke Fasciola hepatica infests mainly ruminants, but it can also cause fasciolosis in people, who ingest the metacercariae encysted on plants. The drug of choice to treat fasciolosis is triclabendazole (TBZ), which has been on the market for several decades. This is also true for the other available drugs.

Drought Sensitivity of Norway Spruce at the Species' Warmest Fringe: Quantitative and Molecular Analysis Reveals High Genetic Variation Among and Within Provenances.

Norway spruce ( is by far the most important timber species in Europe, but its outstanding role in future forests is jeopardized by its high sensitivity to drought. We analyzed drought response of Norway spruce at the warmest fringe of its natural range. Based on a 35-year old provenance experiment we tested for genetic variation among and within seed provenances across consecutively occurring strong drought events using dendroclimatic time series.

Association genetics of phenolic needle compounds in Norway spruce with variable susceptibility to needle bladder rust.

Accumulation of phenolic needle metabolites in Norway spruce is regulated by many genes with small and additive effects and is correlated with the susceptibility against fungal attack. Norway spruce accumulates high foliar concentrations of secondary phenolic metabolites, with important functions for pathogen defence responses. However, the molecular genetic basis underlying the quantitative variation of phenolic compounds and their role in enhanced resistance of spruce to infection by needle bladder rust are unknown.

Selecting Hypomethylated Genomic Regions Using MRE-Seq.

Here, we describe a method capable of filtering the hypomethylated part of plant genomes, the so-called hypomethylome. The principle of the method is based on the filtration and sequence analysis of small DNA fragments generated by methylation-sensitive four-cutter restriction endonucleases, possessing ((5me))CpG motifs in their recognition sites. The majority of these fragments represent genes and their flanking regions containing also regulatory elements-the gene space of the genome.

How to Isolate a Plant's Hypomethylome in One Shot.

Genome assembly remains a challenge for large and/or complex plant genomes due to their abundant repetitive regions resulting in studies focusing on gene space instead of the whole genome. Thus, DNA enrichment strategies facilitate the assembly by increasing the coverage and simultaneously reducing the complexity of the whole genome. In this paper we provide an easy, fast, and cost-effective variant of MRE-seq to obtain a plant's hypomethylome by an optimized methyl filtration protocol followed by next generation sequencing.

Dissecting plant genomes with the PLAZA comparative genomics platform.

With the arrival of low-cost, next-generation sequencing, a multitude of new plant genomes are being publicly released, providing unseen opportunities and challenges for comparative genomics studies. Here, we present PLAZA 2.5, a user-friendly online research environment to explore genomic information from different plants.

Functional annotation of expressed sequence tags as a tool to understand the molecular mechanism controlling flower bud development in tree peony.

Tree peony (Paeonia suffruticosaAndrews) is an important medicinal and ornamental plant. In China, its root bark is an important ingredient for traditional Chinese medicine. It is valued as an ornamental plant because its flower shows a wide variation in shape and color.

Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106.

Leaf hairs (trichomes) of Arabidopsis (Arabidopsis thaliana) have been extensively used as a model to address general questions in cell and developmental biology. Here, we lay the foundation for a systems-level understanding of the biology of this model cell type by performing genome-wide gene expression analyses. We have identified 3,231 genes that are up-regulated in mature trichomes relative to leaves without trichomes, and we compared wild-type trichomes with two mutants, glabra3 and triptychon, that affect trichome morphology and physiology in contrasting ways.

A role for AtWRKY23 in feeding site establishment of plant-parasitic nematodes.

During the interaction between sedentary plant-parasitic nematodes and their host, complex morphological and physiological changes occur in the infected plant tissue, finally resulting in the establishment of a nematode feeding site. This cellular transformation is the result of altered plant gene expression most likely induced by proteins injected in the plant cell by the nematode. Here, we report on the identification of a WRKY transcription factor expressed during nematode infection.