Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication

Decrease of gene expression diversity during domestication of animals and plants

(2019) Wei Liu et al.   BMC EVOLUTIONARY BIOLOGY

Cross-species hybridization and the origin of North African date palms

(2019) Jonathan M. Flowers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physiological, epigenetic and genetic regulation in some olive cultivars under salt stress

(2019) Soraya Mousavi et al.   Scientific Reports

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

Domestication rewired gene expression and nucleotide diversity patterns in tomato

(2017) Christopher Sauvage et al.   PLANT JOURNAL

Assessing elements of an extended evolutionary synthesis for plant domestication and agricultural origin research

(2017) Dolores R. Piperno   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary genomics of grape (Vitis viniferassp.vinifera) domestication

(2017) Yongfeng Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome of wild olive and the evolution of oil biosynthesis

(2017) Turgay Unver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement

(2017) Naibin Duan et al.   Nature Communications

Evolutionary forces affecting synonymous variations in plant genomes

(2017) Yves Clément et al.   PLoS Genetics

Superheroes and masterminds of plant domestication

(2016) Natalia E. Martínez-Ainsworth et al.   COMPTES RENDUS BIOLOGIES

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives

(2016) Gautier Sarah et al.   Molecular Ecology Resources

pcadapt: anRpackage to perform genome scans for selection based on principal component analysis

(2016) Keurcien Luu et al.   Molecular Ecology Resources

De NovoTranscriptome Sequencing ofOlea europaeaL. to Identify Genes Involved in the Development of the Pollen Tube

(2016) Domenico Iaria et al.   TheScientificWorldJOURNAL

Lessons from Domestication: Targeting Cis -Regulatory Elements for Crop Improvement

(2016) Gwen Swinnen et al.   TRENDS IN PLANT SCIENCE

A single generation of domestication heritably alters the expression of hundreds of genes

(2016) Mark R. Christie et al.   Nature Communications

DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening

(2016) Philippe Gallusci et al.   Frontiers in Plant Science

De NovoTranscriptome Sequencing ofOlea europaeaL. to Identify Genes Involved in the Development of the Pollen Tube

(2016) Domenico Iaria et al.   Scientific World Journal

Genome sequence of the olive tree, Olea europaea

(2016) Fernando Cruz et al.   GigaScience

Enhanced seed oil content by overexpressing genes related to triacylglyceride synthesis

(2015) Fang Liu et al.   GENE

Initial Molecular-Level Response to Artificial Selection for Increased Aerobic Metabolism Occurs Primarily through Changes in Gene Expression

(2015) Mateusz Konczal et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data

(2015) Nicolas Duforet-Frebourg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation

(2015) Wolfgang Stephan   MOLECULAR ECOLOGY

Detection of selective sweeps in structured populations: a comparison of recent methods

(2015) Alexandra I. Vatsiou et al.   MOLECULAR ECOLOGY

Single vs multiple independent olive domestications: the jury is (still) out

(2015) Guillaume Besnard et al.   NEW PHYTOLOGIST

The jury may be out, but it is important that it deliberates: a response to Besnard and Rubio de Casas about olive domestication

(2015) Concepción M. Díez et al.   NEW PHYTOLOGIST

Genomics and the Contrasting Dynamics of Annual and Perennial Domestication

(2015) Brandon S. Gaut et al.   TRENDS IN GENETICS

ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome

(2015) Rosario Carmona et al.   Frontiers in Plant Science

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

The contribution of genetic and genomic approaches to plant domestication studies

(2014) Paul Gepts   CURRENT OPINION IN PLANT BIOLOGY

Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves

(2014) María de la O Leyva-Pérez et al.   DNA RESEARCH

SNP2GO: Functional Analysis of Genome-Wide Association Studies

(2014) David Szkiba et al.   GENETICS

The Peculiar Landscape of Repetitive Sequences in the Olive (Olea europaea L.) Genome

(2014) Elena Barghini et al.   Genome Biology and Evolution

Genome Scans for Detecting Footprints of Local Adaptation Using a Bayesian Factor Model

(2014) Nicolas Duforet-Frebourg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima)

(2014) Benoit Nabholz et al.   MOLECULAR ECOLOGY

Evaluation of demographic history and neutral parameterization on the performance ofFSToutlier tests

(2014) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Olive domestication and diversification in the Mediterranean Basin

(2014) Concepcion M. Diez et al.   NEW PHYTOLOGIST

Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean

(2014) E. Bellucci et al.   PLANT CELL

The Role of cis Regulatory Evolution in Maize Domestication

(2014) Zachary H. Lemmon et al.   PLoS Genetics

Population genetics of Mediterranean and Saharan olives: geographic patterns of differentiation and evidence for early generations of admixture

(2013) G. Besnard et al.   ANNALS OF BOTANY

A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes

(2013) Kenneth M. Olsen et al.   Annual Review of Plant Biology

Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation

(2013) Ruben Parra et al.   BMC GENOMICS

De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome

(2013) A. Munoz-Merida et al.   DNA RESEARCH

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

Construction of Core Collections Suitable for Association Mapping to Optimize Use of Mediterranean Olive (Olea europaea L.) Genetic Resources

(2013) Ahmed El Bakkali et al.   PLoS One

QTL Mapping of Flowering and Fruiting Traits in Olive

(2013) Inès Ben Sadok et al.   PLoS One

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

(2013) D. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant

(2013) G. Besnard et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Are olive cultivars distinguishable from oleaster trees based on morphology of drupes and pits, oil composition and microsatellite polymorphisms?

(2013) Hédia Hannachi et al.   ACTA BOTANICA GALLICA

Primary domestication and early uses of the emblematic olive tree: palaeobotanical, historical and molecular evidence from the Middle East

(2012) David Kaniewski et al.   BIOLOGICAL REVIEWS

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Reshaping of the maize transcriptome by domestication

(2012) R. Swanson-Wagner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties

(2012) Amandine Cornille et al.   PLoS Genetics

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

From forest to field: Perennial fruit crop domestication

(2011) Allison J. Miller et al.   AMERICAN JOURNAL OF BOTANY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Genomic profiling of plastid DNA variation in the Mediterranean olive tree

(2011) Guillaume Besnard et al.   BMC PLANT BIOLOGY

Worldwide Core Collection of Olive Cultivars Based on Simple Sequence Repeat and Morphological Markers

(2011) Concepción M. Díez et al.   CROP SCIENCE

Natural epigenetic variation in plant species: a view from the field

(2011) Eric J Richards   CURRENT OPINION IN PLANT BIOLOGY

Genetic structure and core collection of the World Olive Germplasm Bank of Marrakech: towards the optimised management and use of Mediterranean olive genetic resources

(2011) Hicham Haouane et al.   GENETICA

Inference of Mutation Parameters and Selective Constraint in Mammalian Coding Sequences by Approximate Bayesian Computation

(2011) P. D. Keightley et al.   GENETICS

Comparison ofFSToutlier tests for SNP loci under selection

(2011) SHAWN R. NARUM et al.   Molecular Ecology Resources

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Genetic structure and domestication history of the grape

(2011) Sean Myles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Developing a core collection of olive (Olea europaea L.) based on molecular markers (DArTs, SSRs, SNPs) and agronomic traits

(2011) Angjelina Belaj et al.   Tree Genetics & Genomes

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Olea europaea L. in the North Mediterranean Basin during the Pleniglacial and the Early–Middle Holocene

(2010) Yolanda Carrión et al.   QUATERNARY SCIENCE REVIEWS

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The origins of the domestication of the olive tree

(2009) Catherine Breton et al.   COMPTES RENDUS BIOLOGIES

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

A Genomic Scan for Selection Reveals Candidates for Genes Involved in the Evolution of Cultivated Sunflower (Helianthus annuus)

(2008) M. A. Chapman et al.   PLANT CELL