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View article: DNA methylation around transcription start sites not globally associated with transcription in natural and synthetic hexaploid wheat
DNA methylation around transcription start sites not globally associated with transcription in natural and synthetic hexaploid wheat Open
Epigenetic mechanisms including DNA methylation are assumed to play crucial roles in the maintenance of genome integrity, regulation of gene expression and development, and their increasing exploitation in breeding applications is anticipa…
View article: A strategy for studying epigenetic diversity in natural populations: proof of concept in poplar and oak
A strategy for studying epigenetic diversity in natural populations: proof of concept in poplar and oak Open
In the last 20 years, several techniques have been developed for quantifying DNA methylation, the most studied epigenetic marks in eukaryotes, including the gold standard method, whole-genome bisulfite sequencing (WGBS). WGBS quantifies ge…
View article: Bioinformatics manual for population epigenomics combining whole-genome and target genome sequencing v1
Bioinformatics manual for population epigenomics combining whole-genome and target genome sequencing v1 Open
We developed a strategy and a workflow for quantifying epigenetic diversity in natural populations combining whole genome and targeted capture sequencing for DNA methylation. We first identified regions of highly variable DNA methylation i…
View article: Genomic data integration tutorial, a plant case study
Genomic data integration tutorial, a plant case study Open
Background The ongoing evolution of the Next Generation Sequencing (NGS) technologies has led to the production of genomic data on a massive scale. While tools for genomic data integration and analysis are becoming increasingly available, …
View article: Epigenetic Variation in Tree Evolution: a case study in black poplar (<i>Populus nigra</i>)
Epigenetic Variation in Tree Evolution: a case study in black poplar (<i>Populus nigra</i>) Open
SUMMARY How perennial organisms adapt to environments is a key question in biology. To address this question, we investigated ten natural black poplar ( Populus nigra ) populations from Western Europe, a keystone forest tree of riparian ec…
View article: Translational research from models to crops: comparative genomics for plant breeding
Translational research from models to crops: comparative genomics for plant breeding Open
The concept of translational research, which originated in the medical field in the 1980s, consists in improving the efficient transfer of research results obtained in a species (which can be considered as a model or pivot) to all the spec…
View article: SyntenyViewer: a comparative genomics-driven translational research tool
SyntenyViewer: a comparative genomics-driven translational research tool Open
SyntenyViewer is a public web-based tool relying on a relational database available at https://urgi.versailles.inrae.fr/synteny delivering comparative genomics data and associated reservoir of conserved genes between angiosperm species for…
View article: A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs
A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs Open
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for study…
View article: A chromosome-level genome assembly of the European Beech (<i>Fagus sylvatica</i>) reveals anomalies for organelle DNA integration, repeat content and distribution of SNPs
A chromosome-level genome assembly of the European Beech (<i>Fagus sylvatica</i>) reveals anomalies for organelle DNA integration, repeat content and distribution of SNPs Open
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for study…
View article: Additional file 8 of Episodes of gene flow and selection during the evolutionary history of domesticated barley
Additional file 8 of Episodes of gene flow and selection during the evolutionary history of domesticated barley Open
Additional file 8: Table S2. Sweeping of previously identified domestication and improvement genes.
View article: Additional file 9 of Episodes of gene flow and selection during the evolutionary history of domesticated barley
Additional file 9 of Episodes of gene flow and selection during the evolutionary history of domesticated barley Open
Additional file 9: Table S3. Protein-changing variants identified as possible selection targets for each sweep and each group.
View article: Additional file 1 of Episodes of gene flow and selection during the evolutionary history of domesticated barley
Additional file 1 of Episodes of gene flow and selection during the evolutionary history of domesticated barley Open
Additional file 1: Table S1. Barley accessions used in this study.
Identification of a major QTL and associated molecular marker for high arabinoxylan fibre in white wheat flour Open
Dietary fibre (DF) has multiple health benefits and wheat grains are major sources of DF for human health. However, DF is depleted in white wheat flour which is more widely consumed than wholegrain. The major DF component in white flour is…
View article: Genome sequence of the cluster root forming white lupin
Genome sequence of the cluster root forming white lupin Open
White lupin ( Lupinus albus L. ) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch) 1–5 . White …
View article: Identification of a major QTL and associated marker for high arabinoxylan fibre in white wheat flour
Identification of a major QTL and associated marker for high arabinoxylan fibre in white wheat flour Open
Relative viscosity data and total arabinoxylan content derived from enzymatic fingerprinting for the four populations studied: Yumai x Altigo, 2013 Yumai x Claire, 2015, 2016 Yumai x Ukrainka, 2013 Yumai x Valoris, 2013, 2017
View article: Clarifying the role of DNA methylation in tree phenotypic plasticity
Clarifying the role of DNA methylation in tree phenotypic plasticity Open
In a context of global climate change, trees as sessile and long lifespan organisms need to develop mechanisms enablingthem to adapt and to survive. These last years, epigenetic mechanisms such as DNA methylation have been proposed as aval…