Genome assembly and annotation of Arabidopsis halleri , a model for heavy metal hyperaccumulation and evolutionary ecology

Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the AllotetraploidArabidopsis kamchatica

(2016) Timothy Paape et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

(2016) Polina Yu Novikova et al.   NATURE GENETICS

Evolution of Selfing: Recurrent Patterns in Molecular Adaptation

(2015) Kentaro K. Shimizu et al.   Annual Review of Ecology Evolution and Systematics

Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments

(2015) Hiroshi Kudoh   NEW PHYTOLOGIST

A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species

(2015) Shosei Kubota et al.   PLoS Genetics

Zinc and cadmium hyperaccumulation act as deterrents towards specialist herbivores and impede the performance of a generalist herbivore

(2014) Ardeshir Kazemi-Dinan et al.   NEW PHYTOLOGIST

Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis

(2014) Satoru Akama et al.   NUCLEIC ACIDS RESEARCH

Dominance hierarchy arising from the evolution of a complex small RNA regulatory network

(2014) Eléonore Durand et al.   SCIENCE

Genome size variation and evolution in allotetraploid Arabidopsis kamchatica and its parents, Arabidopsis lyrata and Arabidopsis halleri

(2014) Diana E. Wolf et al.   AoB Plants

Frequency-dependent herbivory by a leaf beetle, Phaedon brassicae, on hairy and glabrous plants of Arabidopsis halleri subsp. gemmifera

(2013) Yasuhiro Sato et al.   EVOLUTIONARY ECOLOGY

Population genomic footprints of selection and associations with climate in natural populations ofArabidopsis hallerifrom the Alps

(2013) Martin C. Fischer et al.   MOLECULAR ECOLOGY

Development of anArabis alpinagenomic contig sequence data set and application to single nucleotide polymorphisms discovery

(2013) Stéphane Lobréaux et al.   Molecular Ecology Resources

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

(2013) Tanja Slotte et al.   NATURE GENETICS

Hard Selective Sweep and Ectopic Gene Conversion in a Gene Cluster Affording Environmental Adaptation

(2013) Marc Hanikenne et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis

(2012) Pauline M. Goubet et al.   PLoS Genetics

Recent Loss of Self-Incompatibility by Degradation of the Male Component in Allotetraploid Arabidopsis kamchatica

(2012) Takashi Tsuchimatsu et al.   PLoS Genetics

Current challenges in de novo plant genome sequencing and assembly

(2012) Michael C Schatz et al.   GENOME BIOLOGY

Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology

(2011) Kentaro K. Shimizu et al.   ANNALS OF BOTANY

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Coexistence of Trichome Variation in a Natural Plant Population: A Combined Study Using Ecological and Candidate Gene Approaches

(2011) Tetsuhiro Kawagoe et al.   PLoS One

Does Speciation between Arabidopsis halleri and Arabidopsis lyrata Coincide with Major Changes in a Molecular Target of Adaptation?

(2011) Camille Roux et al.   PLoS One

Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection

(2011) Vincent Castric et al.   PLoS Genetics

Metal Hyperaccumulation in Plants

(2010) Ute Krämer   Annual Review of Plant Biology

The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier

(2010) Roswitha Schmickl et al.   BMC EVOLUTIONARY BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene

(2010) Takashi Tsuchimatsu et al.   NATURE

Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment

(2010) S. Aikawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Five AhMTP1 Zinc Transporters Undergo Different Evolutionary Fates towards Adaptive Evolution to Zinc Tolerance in Arabidopsis halleri

(2010) Zaigham Shahzad et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Power of the Methods for Detecting Interlocus Gene Conversion

(2009) S. P. Mansai et al.   GENETICS

The allopolyploidArabidopsis kamchaticaoriginated from multiple individuals ofArabidopsis lyrataandArabidopsis halleri

(2009) RIE SHIMIZU-INATSUGI et al.   MOLECULAR ECOLOGY

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4

(2008) Marc Hanikenne et al.   NATURE