Homeologue differential expression in the flavonoid biosynthetic pathway underlies flower colour variation in natural and synthetic polyploids of Nicotiana tabacum (Solanaceae)

Subgenome‐dominant expression and alternative splicing in response to Sclerotinia infection in polyploid Brassica napus and progenitors

(2023) Grant W. de Jong et al.   PLANT JOURNAL

The genetic mechanisms underlying the convergent evolution of pollination syndromes in the Neotropical radiation of Costus L.

(2022) Eugenio Valderrama et al.   Frontiers in Plant Science

Lost in translation: Molecular basis of reduced flower coloration in a self-pollinated monkeyflower ( Mimulus ) species

(2022) Mei Liang et al.   Science Advances

LCM and RNA-seq analyses revealed roles of cell cycle and translational regulation and homoeolog expression bias in cotton fiber cell initiation

(2021) Atsumi Ando et al.   BMC GENOMICS

Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)

(2021) Duo Chen et al.   BMC GENOMICS

Genetic architecture of floral traits in bee‐ and hummingbird‐pollinated sister species of Aquilegia (columbine)

(2021) Molly B. Edwards et al.   EVOLUTION

Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize

(2020) Jesse R. Walsh et al.   BMC PLANT BIOLOGY

Increased Flavonol Levels in Tobacco Expressing AcFLS Affect Flower Color and Root Growth

(2020) Sangkyu Park et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The R2R3-MYB transcription factor GhMYB1a regulates flavonol and anthocyanin accumulation in Gerbera hybrida

(2020) Chunmei Zhong et al.   Horticulture Research

Functional characterization of three flavonol synthase genes from Camellia sinensis: roles in flavonol accumulation

(2020) Xiaolan Jiang et al.   PLANT SCIENCE

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

(2020) Shengchen Shan et al.   Frontiers in Genetics

Global insights into duplicated gene expression and alternative splicing in polyploid Brassica napus under heat, cold, and drought stress

(2020) Joon Seon Lee et al.   Plant Genome

Differential Gene Expression with an Emphasis on Floral Organ Size Differences in Natural and Synthetic Polyploids of Nicotiana tabacum (Solanaceae)

(2020) Jacob B. Landis et al.   Genes

Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae)

(2019) Elizabeth W. McCarthy et al.   BMC PLANT BIOLOGY

Identification and Functional Analysis of a Flavonol Synthase Gene from Grape Hyacinth

(2019) Hongli Liu et al.   MOLECULES

Molecular and Functional Characterization of Oryza sativa Flavonol Synthase (OsFLS), a Bifunctional Dioxygenase

(2019) Sangkyu Park et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Expression Level Dominance and Homeolog Expression Bias in Recurrent Origins of the Allopolyploid Fern Polypodium hesperium

(2019) Erin M. Sigel et al.   AMERICAN FERN JOURNAL

Scaling read aligners to hundreds of threads on general-purpose processors

(2018) Ben Langmead et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Evolution of floral traits and impact of reproductive mode on diversification in the phlox family (Polemoniaceae)

(2018) Jacob B. Landis et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

Great Cause—Small Effect: Undeclared Genetically Engineered Orange Petunias Harbor an Inefficient Dihydroflavonol 4-Reductase

(2018) Christian Haselmair-Gosch et al.   Frontiers in Plant Science

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

(2018) Jian Wu et al.   BMC GENOMICS

Parental transposable element loads influence their dynamics in young Nicotiana hybrids and allotetraploids

(2018) Corinne Mhiri et al.   NEW PHYTOLOGIST

Pseudogenization and Resurrection of a Speciation Gene

(2018) Korinna Esfeld et al.   CURRENT BIOLOGY

Cis -trans controls and regulatory novelty accompanying allopolyploidization

(2018) Guanjing Hu et al.   NEW PHYTOLOGIST

Comparative Analysis of Two Flavonol Synthases from Different-Colored Onions Provides Insight into Flavonoid Biosynthesis

(2017) Sangkyu Park et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

A novel R3 MYB transcriptional repressor associated with the loss of floral pigmentation in Iochroma

(2017) Daniel J. Gates et al.   NEW PHYTOLOGIST

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

Concerted Divergence after Gene Duplication in Polycomb Repressive Complexes

(2017) Yichun Qiu et al.   PLANT PHYSIOLOGY

Time-calibrated phylogenetic trees establish a lag between polyploidisation and diversification in Nicotiana (Solanaceae)

(2017) James J. Clarkson et al.   PLANT SYSTEMATICS AND EVOLUTION

Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae

(2016) Tom J. Ellis et al.   ANNALS OF BOTANY

Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis

(2016) Joseph P. Gallagher et al.   MOLECULAR ECOLOGY

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

(2016) Jinghua Yang et al.   NATURE GENETICS

Subgenome-specific assembly of vitamin E biosynthesis genes and expression patterns during seed development provide insight into the evolution of oat genome

(2016) Juan J. Gutierrez-Gonzalez et al.   PLANT BIOTECHNOLOGY JOURNAL

RNAi-mediated suppression of dihydroflavonol 4-reductase in tobacco allows fine-tuning of flower color and flux through the flavonoid biosynthetic pathway

(2016) Sun-Hyung Lim et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea

(2016) Josh Clevenger et al.   Frontiers in Plant Science

The effect of polyploidy and hybridization on the evolution of floral colour inNicotiana(Solanaceae)

(2015) Elizabeth W. McCarthy et al.   ANNALS OF BOTANY

In a world of white, flower colour matters: A white-purple transition signals lack of reward in an alpineEuphrasia

(2015) Vicky J. McGimpsey et al.   AUSTRAL ECOLOGY

Transcriptome asymmetry in synthetic and natural allotetraploid wheats, revealed by RNA-sequencing

(2015) Xutong Wang et al.   NEW PHYTOLOGIST

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

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

Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat

(2015) Andrea L. Harper et al.   PLANT BIOTECHNOLOGY JOURNAL

The Balance of Expression of Dihydroflavonol 4-reductase and Flavonol Synthase Regulates Flavonoid Biosynthesis and Red Foliage Coloration in Crabapples

(2015) Ji Tian et al.   Scientific Reports

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Ecological Transition Predictably Associated with Gene Degeneration

(2014) Carolyn A. Wessinger et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Satoru Akama et al.   NUCLEIC ACIDS RESEARCH

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

Genome interplay in the grain transcriptome of hexaploid bread wheat

(2014) M. Pfeifer et al.   SCIENCE

Comparative Evolutionary and Developmental Dynamics of the Cotton (Gossypium hirsutum) Fiber Transcriptome

(2014) Mi-Jeong Yoo 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

Genetic Dissection of a Major Anthocyanin QTL Contributing to Pollinator-Mediated Reproductive Isolation Between Sister Species ofMimulus

(2013) Yao-Wu Yuan et al.   GENETICS

Functional analyses of a flavonol synthase–like gene from Camellia nitidissima reveal its roles in flavonoid metabolism during floral pigmentation

(2013) Xing-Wen Zhou et al.   JOURNAL OF BIOSCIENCES

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

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

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

RECONSTRUCTING THE COMPLEX EVOLUTIONARY ORIGIN OF WILD ALLOPOLYPLOID TOBACCOS (NICOTIANASECTIONSUAVEOLENTES)

(2012) Laura J. Kelly et al.   EVOLUTION

Homoeolog expression bias and expression level dominance in allopolyploid cotton

(2012) M-J Yoo et al.   HEREDITY

Cloning, Characterization, and Activity Analysis of a Flavonol Synthase Gene FtFLS1 and Its Association with Flavonoid Content in Tartary Buckwheat

(2012) Chenglei Li et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Functional Evolution of an Anthocyanin Pathway Enzyme during a Flower Color Transition

(2012) Stacey D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Characterization of a heavy-ion induced white flower mutant of allotetraploid Nicotiana tabacum

(2012) Yusuke Kazama et al.   PLANT CELL REPORTS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Gene Loss and Parallel Evolution Contribute to Species Difference in Flower Color

(2011) S. D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of two genes causing reinforcement in the Texas wildflower Phlox drummondii

(2011) Robin Hopkins et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids

(2011) Shaowei Dong et al.   NEW PHYTOLOGIST

Cloning and characterization of a UV-B-inducible maize flavonol synthase

(2010) Maria Lorena Falcone Ferreyra et al.   PLANT JOURNAL

Variation in Antiherbivore Defense Responses in Synthetic Nicotiana Allopolyploids Correlates with Changes in Uniparental Patterns of Gene Expression

(2010) S. Anssour et al.   PLANT PHYSIOLOGY

Modulation of Transcriptome and Metabolome of Tobacco by Arabidopsis Transcription Factor, AtMYB12, Leads to Insect Resistance

(2010) P. Misra et al.   PLANT PHYSIOLOGY

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Intragenic Recombination Events and Evidence for Hybrid Speciation in Nicotiana (Solanaceae)

(2009) Laura J. Kelly et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nuclear glutamine synthetase evolution in Nicotiana: Phylogenetics and the origins of allotetraploid and homoploid (diploid) hybrids

(2009) James J. Clarkson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation

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

Genetic changes contributing to the parallel evolution of red floral pigmentation amongIpomoeaspecies

(2009) Matthew A. Streisfeld et al.   NEW PHYTOLOGIST

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

(2008) Lex Flagel et al.   BMC BIOLOGY

Evolutionary Transitions in Floral Color

(2008) Mark D. Rausher   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Functional Analysis of a Predicted Flavonol Synthase Gene Family in Arabidopsis

(2008) D. K. Owens et al.   PLANT PHYSIOLOGY

Metabolomic and genetic analyses of flavonol synthesis in Arabidopsis thaliana support the in vivo involvement of leucoanthocyanidin dioxygenase

(2008) Ralf Stracke et al.   PLANTA