Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed

Variable inbreeding depression may explain associations between the mating system and herbicide resistance in the common morning glory

(2021) Megan L. Van Etten et al.   MOLECULAR ECOLOGY

Reduced phenotypic plasticity evolves in less predictable environments

(2020) Christelle Leung et al.   ECOLOGY LETTERS

Genetic gene expression changes during environmental adaptations tend to reverse plastic changes even after the correction for statistical nonindependence

(2019) Wei-Chin Ho et al.   MOLECULAR BIOLOGY AND EVOLUTION

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Evolutionary and ecological insights from herbicide-resistant weeds: what have we learned about plant adaptation, and what is left to uncover?

(2019) Regina S. Baucom   NEW PHYTOLOGIST

Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

(2019) Daniel R. Kohlhase et al.   BMC PLANT BIOLOGY

A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana

(2019) Neerakkal Sujeeth et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta

(2018) Maggie R. Wagner et al.   EVOLUTION

Contesting the evidence for non-adaptive plasticity

(2018) François Mallard et al.   NATURE

Determining the evolutionary forces shaping G  × E

(2018) Emily B. Josephs   NEW PHYTOLOGIST

Evolutionary adaptations to new environments generally reverse plastic phenotypic changes

(2018) Wei-Chin Ho et al.   Nature Communications

Is plasticity caused by single genes?

(2018) J. van Gestel et al.   NATURE

Harnessing Phenotypic Plasticity to Improve Maize Yields

(2018) Aaron Kusmec et al.   Frontiers in Plant Science

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Leucine-rich repeat extensin proteins regulate plant salt tolerance in Arabidopsis

(2018) Chunzhao Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox

(2017) Alice A. Wright et al.   PLANTA

The effect of artificial selection on phenotypic plasticity in maize

(2017) Joseph L. Gage et al.   Nature Communications

The Arabidopsis leucine-rich repeat receptor kinase MIK2/LRR-KISS connects cell wall integrity sensing, root growth and response to abiotic and biotic stresses

(2017) Dieuwertje Van der Does et al.   PLoS Genetics

Transcriptome Profiling to Identify Genes Involved in Mesosulfuron-Methyl Resistance in Alopecurus aequalis

(2017) Ning Zhao et al.   Frontiers in Plant Science

Does resistance really carry a fitness cost?

(2017) Richard H ffrench-Constant et al.   Current Opinion in Insect Science

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

(2016) Belinda Phipson et al.   Annals of Applied Statistics

Fitness costs of herbicide resistance across natural populations of the common morning glory,Ipomoea purpurea

(2016) Megan L. Van Etten et al.   EVOLUTION

Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4grass

(2016) John T. Lovell et al.   GENOME RESEARCH

Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes

(2016) Yuheng Huang et al.   PLoS Genetics

The geographic mosaic of herbicide resistance evolution in the common morning glory,Ipomoea purpurea: Evidence for resistance hotspots and low genetic differentiation across the landscape

(2015) Adam Kuester et al.   Evolutionary Applications

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature

(2015) Cameron K. Ghalambor et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance

(2015) Arnaud Duhoux et al.   PLANT MOLECULAR BIOLOGY

Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress

(2015) Anne-Antonella Serra et al.   Frontiers in Plant Science

Cryptic genetic variation: evolution's hidden substrate

(2014) Annalise B. Paaby et al.   NATURE REVIEWS GENETICS

Transcriptome Profiling to Discover Putative Genes Associated with Paraquat Resistance in Goosegrass (Eleusine indica L.)

(2014) Jing An et al.   PLoS One

The growth–defense pivot: crisis management in plants mediated by LRR-RK surface receptors

(2014) Youssef Belkhadir et al.   TRENDS IN BIOCHEMICAL SCIENCES

De Novo Assembly and Annotation of the Transcriptome of the Agricultural Weed Ipomoea purpurea Uncovers Gene Expression Changes Associated with Herbicide Resistance

(2014) Trent Leslie et al.   G3-Genes Genomes Genetics

PRL1, an RNA-Binding Protein, Positively Regulates the Accumulation of miRNAs and siRNAs in Arabidopsis

(2014) Shuxin Zhang et al.   PLoS Genetics

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

The Molecular Genetics of Insecticide Resistance

(2013) Richard H. ffrench-Constant   GENETICS

Tracing the Geographic Origins of Weedy Ipomoea purpurea in the Southeastern United States

(2013) Zhou Fang et al.   JOURNAL OF HEREDITY

Deciphering the evolution of herbicide resistance in weeds

(2013) Christophe Délye et al.   TRENDS IN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Experimental evolution

(2012) Tadeusz J. Kawecki et al.   TRENDS IN ECOLOGY & EVOLUTION

Morning glory as a powerful model in ecological genomics: tracing adaptation through both natural and artificial selection

(2011) R S Baucom et al.   HEREDITY

Evolution in Action: Plants Resistant to Herbicides

(2010) Stephen B. Powles et al.   Annual Review of Plant Biology

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

CHARACTERIZING SELECTION ON PHENOTYPIC PLASTICITY IN RESPONSE TO NATURAL ENVIRONMENTAL HETEROGENEITY

(2010) Brooke S. Baythavong et al.   EVOLUTION

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

(2010) A. McKenna et al.   GENOME RESEARCH

Phenotypic plasticity and population viability: the importance of environmental predictability

(2010) T. E. Reed et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson 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

WHEN DO ADAPTIVE PLASTICITY AND GENETIC EVOLUTION PREVENT EXTINCTION OF A DENSITY-REGULATED POPULATION?

(2009) Luis-Miguel Chevin et al.   EVOLUTION

Evolving gene expression: from G to E to G×E

(2009) Andrea Hodgins-Davis et al.   TRENDS IN ECOLOGY & EVOLUTION

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

CONSTRAINTS ON THE EVOLUTION OF TOLERANCE TO HERBICIDE IN THE COMMON MORNING GLORY: RESISTANCE AND TOLERANCE ARE MUTUALLY EXCLUSIVE

(2008) Regina S. Baucom et al.   EVOLUTION