Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae)

The FACT Histone Chaperone: Tuning Gene Transcription in the Chromatin Context to Modulate Plant Growth and Development

(2020) Klaus D. Grasser   Frontiers in Plant Science

Gene Balance Predicts Transcriptional Responses Immediately Following Ploidy Change in Arabidopsis thaliana

(2020) Michael J. Song et al.   PLANT CELL

Do Specialized Cells Play a Major Role in Organic Xenobiotic Detoxification in Higher Plants?

(2020) Armand Cavé-Radet et al.   Frontiers in Plant Science

Transcriptome Dynamics of the Inflorescence in Reciprocally Formed Allopolyploid Tragopogon miscellus (Asteraceae)

(2020) Shengchen Shan et al.   Frontiers in Genetics

Genomics of Evolutionary Novelty in Hybrids and Polyploids

(2020) Gonzalo Nieto Feliner et al.   Frontiers in Genetics

Evolutionary dynamics of transposable elements and satellite DNAs in polyploid Spartina species

(2020) Delphine Giraud et al.   PLANT SCIENCE

Evolution of Mutator transposable elements across eukaryotic diversity

(2019) Mathilde Dupeyron et al.   Mobile DNA

Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass

(2019) Clayton J. Visger et al.   AMERICAN JOURNAL OF BOTANY

OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

(2019) Ling Xu et al.   NUCLEIC ACIDS RESEARCH

Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)

(2019) Dmytro Kryvokhyzha et al.   PLoS Genetics

On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

(2019) Emmanuelle Lerat et al.   Genes

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Supporting Spartina : Interdisciplinary perspective shows Spartina as a distinct solid genus

(2019) Alejandro Bortolus et al.   ECOLOGY

Evolution of small RNA expression following hybridization and allopolyploidization: insights from Spartina species (Poaceae, Chloridoideae)

(2019) Armand Cavé-Radet et al.   PLANT MOLECULAR BIOLOGY

The widespread and overlooked replacement of Spartina maritima by non-indigenous S. anglica and S. townsendii in north-western Adriatic saltmarshes

(2018) Joanne X. W. Wong et al.   BIOLOGICAL INVASIONS

The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation

(2018) Jonathan F Wendel et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Specifications of Targeting Heterochromatin Modifications in Plants

(2018) Jered M. Wendte et al.   Molecular Plant

The causes and consequences of subgenome dominance in hybrids and recent polyploids

(2018) Kevin A. Bird et al.   NEW PHYTOLOGIST

Gene Expression Dominance in Allopolyploids: Hypotheses and Models

(2018) Samuel Bottani et al.   TRENDS IN PLANT SCIENCE

Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus

(2018) Jian Wu et al.   BMC GENOMICS

Cis -trans controls and regulatory novelty accompanying allopolyploidization

(2018) Guanjing Hu et al.   NEW PHYTOLOGIST

Increased tolerance to organic xenobiotics following recent allopolyploidy in Spartina (Poaceae)

(2018) Armand Cavé-Radet et al.   PLANT SCIENCE

Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill

(2017) Marta Robertson et al.   Evolutionary Applications

Modulation of Spartina densiflora plant growth and metal accumulation upon selective inoculation treatments: A comparison of gram negative and gram positive rhizobacteria

(2017) Karina I. Paredes-Páliz et al.   MARINE POLLUTION BULLETIN

Detection of polycyclic aromatic hydrocarbons (PAHs) in Medicago sativa L. by fluorescence microscopy

(2017) Wilber S. Alves et al.   MICRON

Evolution of DMSP (dimethylsulfoniopropionate) biosynthesis pathway: Origin and phylogenetic distribution in polyploid Spartina (Poaceae, Chloridoideae)

(2017) Hélène Rousseau et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower

(2017) Patrick P. Edger et al.   PLANT CELL

Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species (Poaceae)

(2017) Julie Ferreira de Carvalho et al.   PLANT SYSTEMATICS AND EVOLUTION

Polyploidy and the proteome

(2016) Douglas E. Soltis et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Persistence, dispersal and genetic evolution of recently formed Spartina homoploid hybrids and allopolyploids in Southern England

(2016) Dalibor Huska et al.   BIOLOGICAL INVASIONS

Invasive Spartina: lessons and challenges

(2016) Malika Ainouche et al.   BIOLOGICAL INVASIONS

Spartina versicolor Fabre: Another case of Spartina trans-Atlantic introduction?

(2016) A. Baumel et al.   BIOLOGICAL INVASIONS

Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity

(2016) Renesh Bedre et al.   BMC GENOMICS

Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and AllododecaploidSpartinaSpecies (Poaceae)

(2016) Julien Boutte et al.   Genome Biology and Evolution

Plant adaptive radiation mediated by polyploid plasticity in transcriptomes

(2016) Rie Shimizu-Inatsugi et al.   MOLECULAR ECOLOGY

Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress

(2016) Gyoungju Nah et al.   PLoS One

Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

(2015) Peipei Li et al.   BMC BIOINFORMATICS

Salt Glands in the Poaceae Family and Their Relationship to Salinity Tolerance

(2015) Gabriel Céccoli et al.   BOTANICAL REVIEW

Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses

(2015) Fabíola Carvalho Santos et al.   CHROMOSOME RESEARCH

Polyploidy and genome evolution in plants

(2015) Pamela S Soltis et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Stress-induced structural changes in plant chromatin

(2015) Aline V Probst et al.   CURRENT OPINION IN PLANT BIOLOGY

The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating

(2015) M. Rousseau-Gueutin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

(2015) David C. Tank et al.   NEW PHYTOLOGIST

Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression

(2015) Jie Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

(2015) Julien Boutte et al.   G3-Genes Genomes Genetics

Nonadditive Gene Expression in Polyploids

(2014) Mi-Jeong Yoo et al.   Annual Review of Genetics

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

Overexpression of maize chloride channel gene ZmCLC-d in Arabidopsis thaliana improved its stress resistance

(2014) S. Wang et al.   BIOLOGIA PLANTARUM

Variation in transcriptome size: are we getting the message?

(2014) Jeremy E. Coate et al.   CHROMOSOMA

Water relations of an invasive halophyte (Spartina patens): osmoregulation and ionic effects on xylem hydraulics

(2014) Valentino Casolo et al.   FUNCTIONAL PLANT BIOLOGY

Extensive Translational Regulation of Gene Expression in an Allopolyploid (Glycine dolichocarpa)

(2014) J. E. Coate et al.   PLANT CELL

Deciphering the molecular bases for drought tolerance inArabidopsisautotetraploids

(2014) JUAN C. DEL POZO et al.   PLANT CELL AND ENVIRONMENT

A molecular phylogeny and new subgeneric classification of Sporobolus (Poaceae: Chloridoideae: Sporobolinae)

(2014) Paul M. Peterson et al.   TAXON

Ecological and Evolutionary Misadventures ofSpartina

(2013) Donald R. Strong et al.   Annual Review of Ecology Evolution and Systematics

Classification and Comparison of Small RNAs from Plants

(2013) Michael J. Axtell   Annual Review of Plant Biology

Natural Pathways to Polyploidy in Plants and Consequences for Genome Reorganization

(2013) A. Tayalé et al.   CYTOGENETIC AND GENOME RESEARCH

Two Evolutionarily Distinct Classes of Paleopolyploidy

(2013) Olivier Garsmeur et al.   MOLECULAR BIOLOGY AND EVOLUTION

Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploidCoffea arabicagrown at contrasted temperatures

(2013) Marie-Christine Combes et al.   NEW PHYTOLOGIST

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Thellungiella salsuginea Tonoplast Aquaporin TsTIP1;2 Functions in Protection Against Multiple Abiotic Stresses

(2013) Li-Li Wang et al.   PLANT AND CELL PHYSIOLOGY

Genome-wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat

(2013) Smadar Ben-David et al.   PLANT JOURNAL

Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis

(2013) J. Ferreira de Carvalho et al.   PLANT MOLECULAR BIOLOGY

Next-generation sequencing and genome evolution in allopolyploids

(2012) Richard J. A. Buggs et al.   AMERICAN JOURNAL OF BOTANY

Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus

(2012) Janet Higgins et al.   BMC GENOMICS

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)

(2012) J Ferreira de Carvalho et al.   HEREDITY

Polyploidy and its effect on evolutionary success: old questions revisited with new tools

(2012) A Madlung   HEREDITY

Homoeolog expression bias and expression level dominance in allopolyploid cotton

(2012) M-J Yoo et al.   HEREDITY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Homoeolog expression bias and expression level dominance in allopolyploids

(2012) C. E. Grover et al.   NEW PHYTOLOGIST

Mobilization of Stowaway-like MITEs in newly formed allohexaploid wheat species

(2012) Beery Yaakov et al.   PLANT MOLECULAR BIOLOGY

Transcriptome and methylome interactions in rice hybrids

(2012) Ramakrishna K. Chodavarapu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematics and management of natural resources: the case of Spartina species on European shores

(2011) José Prieto et al.   BIOLOGIA

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Transcriptomic Shock Generates Evolutionary Novelty in a Newly Formed, Natural Allopolyploid Plant

(2011) Richard J.A. Buggs et al.   CURRENT BIOLOGY

Spartina densiflora demonstrates high tolerance to phenanthrene in soil and reduces it concentration

(2011) Susana Redondo-Gómez et al.   MARINE POLLUTION BULLETIN

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flow cytometry and GISH reveal mixed ploidy populations and Spartina nonaploids with genomes of S. alterniflora and S. maritima origin

(2010) Simon Renny-Byfield et al.   ANNALS OF BOTANY

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Homoeolog-specific transcriptional bias in allopolyploid wheat

(2010) Alina R Akhunova et al.   BMC GENOMICS

Quantifying Whole Transcriptome Size, a Prerequisite for Understanding Transcriptome Evolution Across Species: An Example from a Plant Allopolyploid

(2010) Jeremy E. Coate et al.   Genome Biology and Evolution

Accumulation and tolerance characteristics of chromium in a cordgrass Cr-hyperaccumulator, Spartina argentinensis

(2010) Susana Redondo-Gómez et al.   JOURNAL OF HAZARDOUS MATERIALS

Transcriptome divergence between the hexaploid salt-marsh sister species Spartina maritima and Spartina alterniflora (Poaceae)

(2010) H. CHELAIFA et al.   MOLECULAR ECOLOGY

Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae)

(2010) Houda Chelaifa et al.   NEW PHYTOLOGIST

Mobilization of retrotransposons in synthetic allotetraploid tobacco

(2010) M. Petit et al.   NEW PHYTOLOGIST

Evolutionary consequences of autopolyploidy

(2010) Christian Parisod et al.   NEW PHYTOLOGIST

Investigation of the Transcriptome of Prairie Cord Grass, a New Cellulosic Biomass Crop

(2010) Kristene Gedye et al.   Plant Genome

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genomic and expression plasticity of polyploidy

(2009) Scott Jackson et al.   CURRENT OPINION IN PLANT BIOLOGY

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

Diversity in leaf anatomy, and stomatal distribution and conductance, between salt marsh and freshwater species in the C4 genus Spartina (Poaceae)

(2009) Brian R. Maricle et al.   NEW PHYTOLOGIST

Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina

(2009) Christian Parisod et al.   NEW PHYTOLOGIST

Impact of transposable elements on the organization and function of allopolyploid genomes

(2009) Christian Parisod et al.   NEW PHYTOLOGIST

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

Duplicate genes increase expression diversity in closely related species and allopolyploids

(2009) M. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary Genetics of Genome Merger and Doubling in Plants

(2008) Jeff J. Doyle et al.   Annual Review of Genetics

Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae)

(2008) M. L. Ainouche et al.   BIOLOGICAL INVASIONS

Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution

(2008) Lex Flagel et al.   BMC BIOLOGY

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

Growth and photosynthetic responses to zinc stress of an invasive cordgrass,Spartina densiflora

(2008) E. Mateos-Naranjo et al.   PLANT BIOLOGY