Erwan Guichoux
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View article: Sequencing, de novo assembly of Ludwigia plastomes, and comparative analysis within the Onagraceae family
Sequencing, de novo assembly of Ludwigia plastomes, and comparative analysis within the Onagraceae family Open
The Onagraceae family, which belongs to the order Myrtales, consists of approximately 657 species and 17 genera. This family includes the genus Ludwigia L., which is comprised of 82 species. In this study, we focused on the two aquatic inv…
View article: Data paper: Dataset describing the effects of environmental enrichment and sows’ characteristics on the peripheral blood mononuclear cell transcriptome
Data paper: Dataset describing the effects of environmental enrichment and sows’ characteristics on the peripheral blood mononuclear cell transcriptome Open
International audience
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: Conserving genomic diversity in tropical trees from French Guiana
Conserving genomic diversity in tropical trees from French Guiana Open
International audience
View article: A DNA-capture approach for detection and genome-wide sequencing of Flavescence dorée phytoplasma
A DNA-capture approach for detection and genome-wide sequencing of Flavescence dorée phytoplasma Open
International audience
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: Low-frequency somatic mutations are heritable in tropical trees <i>Dicorynia guianensis</i> and <i>Sextonia rubra</i>
Low-frequency somatic mutations are heritable in tropical trees <i>Dicorynia guianensis</i> and <i>Sextonia rubra</i> Open
Somatic mutations potentially play a role in plant evolution, but common expectations pertaining to plant somatic mutations remain insufficiently tested. Unlike in most animals, the plant germline is assumed to be set aside late in develop…
View article: Reviews of “Whole-genome screening for near-diagnostic genetic markers for four western European white oak species identification“
Reviews of “Whole-genome screening for near-diagnostic genetic markers for four western European white oak species identification“ Open
Reviews of “Whole-genome screening for near-diagnostic genetic markers for four western European white oak species identification“
View article: Whole-genome screening for near-diagnostic genetic markers for white oak species identification in Europe
Whole-genome screening for near-diagnostic genetic markers for white oak species identification in Europe Open
Context Identifying species in the European white oak complex has been a long standing concern in taxonomy, evolution, forest research and management. Quercus petraea, Q. robur, Q. pubescens and Q. pyrenaica are part of this species comple…
View article: Sequencing, de novo assembly of <i>Ludwigia</i> plastomes, and comparative analysis within the Onagraceae family
Sequencing, de novo assembly of <i>Ludwigia</i> plastomes, and comparative analysis within the Onagraceae family Open
The Onagraceae family, which belongs to the order Myrtales, consists of approximately 657 species and 17 genera. This family includes the genus Ludwigia L., which is comprised of 82 species. In this study, we focused on the two aquatic inv…
View article: Comparative genomics of Mycoplasma feriruminatoris, a fast-growing pathogen of wild Caprinae
Comparative genomics of Mycoplasma feriruminatoris, a fast-growing pathogen of wild Caprinae Open
Mycoplasma feriruminatoris is a fast-growing Mycoplasma species isolated from wild Caprinae and first described in 2013. M. feriruminatoris isolates have been associated with arthritis, kerato conjunctivitis, pneumonia and septicemia, but …
View article: Microbial biomarkers of tree water status for next‐generation biomonitoring of forest ecosystems
Microbial biomarkers of tree water status for next‐generation biomonitoring of forest ecosystems Open
Next‐generation biomonitoring proposes to combine machine‐learning algorithms with environmental DNA data to automate the monitoring of the Earth's major ecosystems. In the present study, we searched for molecular biomarkers of tree water …
View article: Plant mutations: slaying beautiful hypotheses by surprising evidence
Plant mutations: slaying beautiful hypotheses by surprising evidence Open
International audience
View article: The genome and population genomics of allopolyploid<i>Coffea arabica</i>reveal the diversification history of modern coffee cultivars
The genome and population genomics of allopolyploid<i>Coffea arabica</i>reveal the diversification history of modern coffee cultivars Open
Coffea arabica , an allotetraploid hybrid of C. eugenioides and C. canephora , is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromos…
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: Evolution of the pattern of Fusarium species infecting French wheat over 15 years: first results
Evolution of the pattern of Fusarium species infecting French wheat over 15 years: first results Open
International audience
View article: Low-frequency somatic mutations are heritable in tropical trees<i>Dicorynia guianensis</i>and<i>Sextonia rubra</i>
Low-frequency somatic mutations are heritable in tropical trees<i>Dicorynia guianensis</i>and<i>Sextonia rubra</i> Open
Somatic mutations potentially play a role in plant evolution, but common expectations pertaining to plant somatic mutations remain insufficiently tested. Unlike in most animals, the plant germline is assumed to be set aside late in develop…
View article: Comparative genomics of<i>Mycoplasma feriruminatoris</i>, a fast-growing pathogen of wild<i>Caprinae</i>
Comparative genomics of<i>Mycoplasma feriruminatoris</i>, a fast-growing pathogen of wild<i>Caprinae</i> Open
Mycoplasma feriruminatoris is a fast-growing Mycoplasma species isolated from wild Caprinae and first described in 2013. M. feriruminatoris isolates have been associated with arthritis, keratoconjunctivitis, pneumonia and septicemia, but w…
View article: Leaf Microbiome Data for European Cultivated Grapevine (<i>Vitis</i> <i>vinifera</i>) During Downy Mildew (<i>Plasmopara viticola</i>) Epidemics in Three Wine-Producing Regions in France
Leaf Microbiome Data for European Cultivated Grapevine (<i>Vitis</i> <i>vinifera</i>) During Downy Mildew (<i>Plasmopara viticola</i>) Epidemics in Three Wine-Producing Regions in France Open
Grapevine downy mildew ( Plasmopara viticola) is a major disease of European cultivated grapevine ( Vitis vinifera L.) against which a large amount of synthetic pesticides are used. Developing microbial biocontrol of P. viticola could redu…
View article: The effect of the 7R allele on the DRD4 risk tolerance locus is independent of background risk in Senegalese fishermen
The effect of the 7R allele on the DRD4 risk tolerance locus is independent of background risk in Senegalese fishermen Open
It has been shown that living in risky environments, as well as having a risky occupation, can moderate risk-tolerance. Despite the involvement of dopamine in the expectation of reward described by neurobiologists, a GWAS study was not abl…
View article: Metagenomic Next-Generation Sequencing (mNGS) Data Reveal the Phyllosphere Microbiome of Wheat Plants Infected by the Fungal Pathogen<i>Zymoseptoria tritici</i>
Metagenomic Next-Generation Sequencing (mNGS) Data Reveal the Phyllosphere Microbiome of Wheat Plants Infected by the Fungal Pathogen<i>Zymoseptoria tritici</i> Open
The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol, or facilitating agents that…
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: NGS data reveals the phyllosphere microbiome of wheat plants infected by the fungal pathogen <i>Zymoseptoria tritici</i>
NGS data reveals the phyllosphere microbiome of wheat plants infected by the fungal pathogen <i>Zymoseptoria tritici</i> Open
The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol or facilitating agents that …