Peter Civáň
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View article: Author Correction: Striking convergent selection history of wheat and barley and its potential for breeding
Author Correction: Striking convergent selection history of wheat and barley and its potential for breeding Open
Correction to: Nature Plantshttps://doi.org/10.1038/s41477-025-02128-0, published online 14 November 2025. In the version of the article initially published, the surname of Manon Delahaye appeared incorrectly (as Delayhe) and has now been …
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: Genetic erosion in domesticated barley and a hypothesis of a North African centre of diversity
Genetic erosion in domesticated barley and a hypothesis of a North African centre of diversity Open
Barley is one of the founder crops of the Neolithic transition in West Asia. While recent advances in genomics have provided a rather detailed picture of barley domestication, there are contradictory views on how the domestication process …
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: 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: Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data
Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data Open
Recently, entire genebank collections of wheat have been extensively characterized with sequencing data. We have identified introgressions using these genotyping-by-sequencing and whole-genome sequencing data. On the basis of our results, …
View article: Meeting the Challenges Facing Wheat Production: The Strategic Research Agenda of the Global Wheat Initiative
Meeting the Challenges Facing Wheat Production: The Strategic Research Agenda of the Global Wheat Initiative Open
Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recogn…
View article: Diversity of Sodium Transporter HKT1;5 in Genus Oryza
Diversity of Sodium Transporter HKT1;5 in Genus Oryza Open
Asian cultivated rice shows allelic variation in sodium transporter, OsHKT1;5, correlating with shoot sodium exclusion (salinity tolerance). These changes map to intra/extracellularly-oriented loops that occur between four transmembrane-P …
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.
View article: data from "The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models"
data from "The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models" Open
The nucleotide, codon-degenerate and protein concatenated alignments of 83 chloroplast genes, with the respective character sets, in nexus format.
View article: data from "The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models"
data from "The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models" Open
The nucleotide, codon-degenerate and protein concatenated alignments of 83 chloroplast genes, with the respective character sets, in nexus format.
View article: Peer Review #2 of "The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models (v0.2)"
Peer Review #2 of "The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models (v0.2)" Open
Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics.Recent analyses of both nuclear and chloroplast genome data of land plan…
View article: Data from the article "The mitochondrial phylogeny of land plants shows support for Setaphyta under non-stationary substitution models"
Data from the article "The mitochondrial phylogeny of land plants shows support for Setaphyta under non-stationary substitution models" Open
Data from the article: "The mitochondrial phylogeny of land plants shows support for Setaphyta under non-stationary substitution models" Filipe de Sousa, Peter Civáň, João Brazão, Peter G. Foster, Cymon J. Cox These data are divided in fou…
View article: Origin of the <i>Aromatic</i> Group of Cultivated Rice (<i>Oryza sativa</i> L.) Traced to the Indian Subcontinent
Origin of the <i>Aromatic</i> Group of Cultivated Rice (<i>Oryza sativa</i> L.) Traced to the Indian Subcontinent Open
The aromatic group of Asian cultivated rice is a distinct population with considerable genetic diversity on the Indian subcontinent and includes the popular Basmati types characterized by pleasant fragrance. Genetic and phenotypic associat…
View article: Barley Exome Diversity
Barley Exome Diversity Open
These are the data sets produced and analyzed by P. Civáň, K. Drosou, D. Armisen-Gimenez, W. Duchemin, J. Salse and T.A. Brown as part of the ADAPT project (European Research Council grant 339941 awarded to T.A. Brown). 320 exome-capture l…
View article: Misconceptions Regarding the Role of Introgression in the Origin of Oryza sativa subsp. indica
Misconceptions Regarding the Role of Introgression in the Origin of Oryza sativa subsp. indica Open
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View article: Comment on ‘Multiple Origin but Single Domestication Led to <i>Oryza sativa</i>’
Comment on ‘Multiple Origin but Single Domestication Led to <i>Oryza sativa</i>’ Open
In 2015, we published an analysis of rice genomic data and showed that the japonica , indica and aus groups of cultivated rice were independently domesticated. Our conclusions were controversial as they contradicted a previous, high-profil…
View article: A novel mutation conferring the nonbrittle phenotype of cultivated barley
A novel mutation conferring the nonbrittle phenotype of cultivated barley Open
Summary The nonbrittle rachis, resulting in a seed head which does not shatter at maturity, is one of the key phenotypes that distinguishes domesticated barley from its wild relatives. The phenotype is associated with two loci, Btr1 and Bt…