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1. Full Text Usability of reference-free transcriptome assemblies for detection of differential expression : A case study on Aethionema arabicum dimorphic seeds
by Wilhelmsson, Per K.I and Chandler, Jake O and Fernandez-Pozo, Noe and Graeber, Kai and Ullrich, Kristian K and Arshad, Waheed and Khan, Safina and Hofberger, Johannes A and Buchta, Karl and Edger, Patrick P and Pires, J.C and Schranz, M.E and Leubner-Metzger, Gerhard and Rensing, Stefan A
BMC Genomics, ISSN 1471-2164, 2019, Volume 20, Issue 1, pp. 95 - 19
Background: RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum... 
RNA-seq | Aethionema arabicum | Reference and reference-free | Dimorphic seeds | Transcriptome | ARABIDOPSIS-THALIANA | CHROMATIN LANDSCAPE | MATURATION | GERMINATION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BRASSICA-NAPUS | GENETICS & HEREDITY | GENE-EXPRESSION | DYNAMICS | GENERATION | REVEALS | RNA sequencing | Usage | Seeds | Cruciferae | Genetic research | Genetic aspects | Research | Gene expression | RNA | Germination | Genes | Genomics | Genomes | DNA binding proteins | Genetic transcription | Case studies | Arabidopsis thaliana | Analysis | Histones
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2. Full Text Disease Resistance Genetics and Genomics in Octoploid Strawberry
by Barbey, CR and Lee, S and Verma, S and Bird, KA and Yocca, AE and Edger, PP and Knapp, SJ and Whitaker, VM and Folta, KM
G3-GENES GENOMES GENETICS, ISSN 2160-1836, 10/2019, Volume 9, Issue 10, pp. 3315 - 3332
Octoploid strawberry (Fragaria xananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to... 
SYSTEM | Disease Resistance | PHYLOGENETIC ANALYSIS | R-gene | eQTL | RenSeq | CONFERRING RESISTANCE | Strawberry | Subgenome Dominance | POWDERY MILDEW | GENETICS & HEREDITY | ECTOPIC EXPRESSION | DOSAGE-SENSITIVITY | TOOL
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3. Full Text Genome-wide association mapping uncovers Fw1, a dominant gene conferring resistance to Fusarium wilt in strawberry
by A. Pincot, Dominique D and Poorten, Thomas J and Hardigan, Michael A and Harshman, Julia M and Acharya, Charlotte B and Cole, Glenn S and Gordon, Thomas R and Stueven, Michelle and Edger, Patrick P and Knapp, Steven J
G3: Genes, Genomes, Genetics, ISSN 2160-1836, 05/2018, Volume 8, Issue 5, pp. 1817 - 1828
Fusarium wilt, a soil-borne disease caused by the fungal pathogen Fusarium oxysporum f. sp. fragariae, threatens strawberry (Fragaria x ananassa) production... 
Innate immunity | Fragaria | Fusarium wilt | Strawberry | Polyploid | PLANT | strawberry | polyploid | LOCUS | POPULATION-GENETICS | innate immunity | F-SP FRAGARIAE | OXYSPORUM | GENETICS & HEREDITY | CULTIVAR RESPONSES | METHYL-BROMIDE | ARABIDOPSIS | TOMATO | PATHOGENS
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4. Full Text Domestication of Temperate and Coastal Hybrids with Distinct Ancestral Gene Selection in Octoploid Strawberry
by Hardigan, Michael A and Poorten, Thomas J and Acharya, Charlotte B and Cole, Glenn S and Hummer, Kim E and Bassil, Nahla and Edger, Patrick P and Knapp, Steven J
The Plant Genome, ISSN 1940-3372, 11/2018, Volume 11, Issue 3, pp. 1 - 11
Core Ideas Genetic restructuring yielded distinct temperate and coastal‐adapted subpopulations. Ancestral species selection bias was discovered in temperate... 
VIRGINIANA | NUMBER | ROSACEAE | FRUIT | FRAGARIA-CHILOENSIS | GENETICS & HEREDITY | DIVERSITY | PLANT SCIENCES
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5. Full Text Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution
by Delaux, Pierre-Marc and Varala, Kranthi and Edger, Patrick P and Coruzzi, Gloria M and Pires, J. Chris and Ané, Jean-Michel
PLoS Genetics, ISSN 1553-7390, 2014, Volume 10, Issue 7, p. e1004487
Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and... 
PHOSPHATE | MEDICAGO-TRUNCATULA | ARBUSCULAR MYCORRHIZAL FUNGI | PAPAYA | GENETICS & HEREDITY | PLANTS | RHIZOBIA | COLONIZATION | GUT MICROBIOTA | ARABIDOPSIS | EXPRESSION | Arabidopsis - genetics | Arabidopsis - microbiology | Mycorrhizae - genetics | Genomics | Phylogeny | Gene Regulatory Networks | Mycorrhizae - growth & development | Evolution, Molecular | Symbiosis - genetics | Arabidopsis thaliana | Physiological aspects | Genetic research | Evolution | Genetic aspects | Research | Plants | Seeds | Flowers & plants
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6. Full Text Early allopolyploid evolution in the post-neolithic Brassica napus oilseed genome
by Chalhoub, Boulos and Denoeud, France and Liu, Shengyi and Parkin, Isobel A. P and Tang, Haibao and Wang, Xiyin and Chiquet, Julien and Belcram, Harry and Tong, Chaobo and Samans, Birgit and Corréa, Margot and Da Silva, Corinne and Just, Jérémy and Falentin, Cyril and Koh, Chu Shin and Le Clainche, Isabelle and Bernard, Maria and Bento, Pascal and Noel, Benjamin and Labadie, Karine and Alberti, Adriana and Charles, Mathieu and Arnaud, Dominique and Guo, Hui and Daviaud, Christian and Alamery, Salman and Jabbari, Kamel and Zhao, Meixia and Edger, Patrick P and Chelaifa, Houda and Tack, David and Lassalle, Gilles and Mestiri, Imen and Schnel, Nicolas and Le Paslier, Marie-Christine and Fan, Guangyi and Renault, Victor and Bayer, Philippe E and Golicz, Agnieszka A and Manoli, Sahana and Lee, Tae-Ho and Thi, Vinh Ha Dinh and Chalabi, Smahane and Hu, Qiong and Fan, Chuchuan and Tollenaere, Reece and Lu, Yunhai and Battail, Christophe and Shen, Jinxiong and Sidebottom, Christine H. D and Wang, Xinfa and Canaguier, Aurélie and Chauveau, Aurélie and Bérard, Aurélie and Deniot, Gwenaëlle and Guan, Mei and Liu, Zhongsong and Sun, Fengming and Lim, Yong Pyo and Lyons, Eric and Town, Christopher D and Bancroft, Ian and Wang, Xiaowu and Meng, Jinling and Ma, Jianxin and Pires, J. Chris and King, Graham J and Brunel, Dominique and Delourme, Régine and Renard, Michel and Aury, Jean-Marc and Adams, Keith L and Batley, Jacqueline and Snowdon, Rod J and Tost, Jorg and Edwards, David and Zhou, Yongming and Hua, Wei and Sharpe, Andrew G and Paterson, Andrew H and Guan, Chunyun and Wincker, Patrick
Science, ISSN 0036-8075, 08/2014, Volume 345, Issue 6199, pp. 950 - 953
Oilseed rape (Brassica napus L.) was formed similar to 7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a... 
PLANT | DOMINANCE | GENE | MULTIDISCIPLINARY SCIENCES | COTTON | Rape (Plant) | Genetic research | Botanical research | Polyploidy | Genetic aspects | Research | Hybridization | Evolutionary biology | Genomics | Rape plants | Rape | Brassica | Genes | Crops | Genetics | Evolution | Genomes | Oilseeds | Life Sciences
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7. Full Text Gene and genome duplications: The impact of dosage-sensitivity on the fate of nuclear genes
by Edger, Patrick P and Pires, J. Chris
Chromosome Research, ISSN 0967-3849, 07/2009, Volume 17, Issue 5, pp. 699 - 717
Whole genome duplications (WGDs) followed by diploidization, which includes gene loss, have been an important recurrent process in the evolution of higher... 
Paleopolyploidy | Subfunctionalization | Polyploidy | Gene Balance | Diploidization | Dosage Compensation | PROTEIN | BIOCHEMISTRY & MOLECULAR BIOLOGY | HOX CLUSTERS | AMPHIOXUS GENOME | VERTEBRATE GENOME | EVOLUTION | GENETICS & HEREDITY | ANCIENT | ARABIDOPSIS | FUNCTIONAL DIVERGENCE | EXPRESSION | Gene Duplication | Dosage Compensation, Genetic | Animals | Nuclear Proteins - genetics | Humans | Mass extinction theory | Anopheles | DNA binding proteins | Endangered species | Analysis | Genomics | Eukaryotes | Flowers & plants | Chromosomes
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8. Full Text The butterfly plant arms-race escalated by gene and genome duplications
by Patrick P. Edger and Hanna M. Heidel-Fischer and Michaël Bekaert and Jadranka Rota and Gernot Glöckner and Adrian E. Platts and David G. Heckel and Joshua P. Der and Eric K. Wafula and Michelle Tang and Johannes A. Hofberger and Ann Smithson and Jocelyn C. Hall and Matthieu Blanchette and Thomas E. Bureau and Stephen I. Wright and Claude W. dePamphilis and M. Eric Schranz and Michael S. Barker and Gavin C. Conant and Niklas Wahlberg and Heiko Vogel and J. Chris Pires and Christopher W. Wheat and Stockholms universitet and Naturvetenskapliga fakulteten and Zoologiska institutionen
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 7/2015, Volume 112, Issue 27, pp. 8362 - 8366
Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the... 
expression | cytochrome-p450 | pieridae | Insecta | polymorphism | papilionidae | Evolutie en fylogenie | fylogenie | arabidopsis | diversificatie | evolutionary genetics | speciation | diversity | co-evolutie | defense | evolutionaire genetica | coevolution | glucosinolates | glucosinolaten | phylogeny | Evolution and Phylogeny | metabolism | diversification | brassica | Evolutionary novelty | Chemical defenses | Coevolution | Diversification | Phylogenomics | DEFENSE | CYTOCHROME-P450 | MULTIDISCIPLINARY SCIENCES | POLYMORPHISM | evolutionary novelty | chemical defenses | METABOLISM | SPECIATION | DIVERSITY | ARABIDOPSIS | EXPRESSION | phylogenomics | Gene Duplication | Butterflies - classification | Gene Expression | Genes, Insect - genetics | Genome, Plant - genetics | Species Specificity | Butterflies - genetics | Genome, Insect - genetics | Insect Proteins - genetics | Phylogeny | Biodiversity | Brassicaceae - genetics | Genetic Variation | Plant Proteins - genetics | Host-Parasite Interactions - genetics | Animals | Genes, Plant - genetics | Brassicaceae - classification | Butterflies - physiology | Bayes Theorem | Brassicaceae - parasitology | Evolution, Molecular | Genetic aspects | Agricultural diversification | Research | Biological Sciences | Medical and Health Sciences | Agricultural Biotechnology | Medicin och hälsovetenskap | Lantbruksvetenskaper | Medicinsk bioteknologi | Agricultural Sciences | Bioteknologi med applikationer på växter och djur | Medical Biotechnology | Naturvetenskap | Biologiska vetenskaper | Natural Sciences
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9. Full Text An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
by Haudry, Annabelle and Platts, Adrian E and Vello, Emilio and Hoen, Douglas R and Leclercq, Mickael and Williamson, Robert J and Forczek, Ewa and Joly-Lopez, Zoé and Steffen, Joshua G and Hazzouri, Khaled M and Dewar, Ken and Stinchcombe, John R and Schoen, Daniel J and Wang, Xiaowu and Schmutz, Jeremy and Town, Christopher D and Edger, Patrick P and Pires, J Chris and Schumaker, Karen S and Jarvis, David E and Mandáková, Terezie and Lysak, Martin A and Van Den Bergh, Erik and Schranz, M Eric and Harrison, Paul M and Moses, Alan M and Bureau, Thomas E and Wright, Stephen I and Blanchette, Mathieu and Joint Genome Institute (JGI)
Nature Genetics, ISSN 1061-4036, 08/2013, Volume 45, Issue 8, pp. 891 - 898
Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains... 
ARABIDOPSIS-THALIANA | HUMAN GENOME | EVOLUTION | ANNOTATION | ULTRACONSERVED ELEMENTS | SIZE | GENETICS & HEREDITY | DNA ELEMENTS | GENE-EXPRESSION | BRASSICA-OLERACEA | DROSOPHILA | Gene Duplication | Genomics | Molecular Sequence Annotation | Regulatory Sequences, Nucleic Acid | Computational Biology | Selection, Genetic | Genome, Plant | Phylogeny | Arabidopsis - genetics | Brassicaceae - genetics | Nucleotide Motifs | Brassicaceae - classification | Gene Deletion | Gene Expression Regulation, Plant | Conserved Sequence | High-Throughput Nucleotide Sequencing | Cluster Analysis | Evolution, Molecular | Noncoding DNA | Physiological aspects | Molecular evolution | Genetic aspects | Research | Cruciferae | Proteins | Phylogenetics | Evolution | Genomes | Deoxyribonucleic acid--DNA | Life Sciences | Populations and Evolution | Genetics | Biodiversity | Systematics, Phylogenetics and taxonomy | Quantitative Methods
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10. Full Text Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis
by Michaël Bekaert and Patrick P. Edger and Corey M. Hudson and J. Chris Pires and Gavin C. Conant
New Phytologist, ISSN 0028-646X, 10/2012, Volume 196, Issue 2, pp. 596 - 605
Here, we describe our updated mathematical model of Columbia metabolism, which adds the glucosinolates, an important group of secondary metabolites, to the... 
Full papers | Enzymes | Capital costs | Biomass production | Glucosinolates | Biosynthesis | Photons | Plants | Herbivores | Metabolism | Plant cells | Arabidopsis thaliana | adaptation | costly traits | flux balance analysis | metabolic network | Flux balance analysis | Metabolic network | Costly traits | Adaptation | BENZOIC-ACID | ARABIDOPSIS-THALIANA | NETWORK | PLANT SCIENCES | NATURAL ENEMIES | BRASSICA-RAPA | BIOSYNTHESIS | PLANT DEFENSE | GENE-EXPRESSION | RESISTANCE | INSECT HERBIVORY | Gene Duplication | Arabidopsis - immunology | Biomass | Systems Biology | Metabolome - genetics | Arabidopsis - metabolism | Arabidopsis - genetics | Biological Evolution | Glucosinolates - biosynthesis | Amino Acids - metabolism | Biosynthetic Pathways - genetics | Herbivory - genetics | Models, Biological | Gene Expression Regulation, Plant | Defense industry | Evolutionary biology | Analysis | Physiological aspects | Evolution | Plant metabolites | Costs | Fluctuations | Biological evolution | Flux | Herbivory | Biology | Metabolic flux | Secondary metabolites | Metabolites | Cost analysis | Photosynthesis | Chemical synthesis
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