Gradual evolution of allopolyploidy in Arabidopsis suecica

One subgenome to rule them all: underlying mechanisms of subgenome dominance

(2020) Elizabeth I Alger et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

(2020) Gai Huang et al.   NATURE GENETICS

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

(2020) Z. Jeffrey Chen et al.   NATURE GENETICS

Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa

(2020) Chris Morgan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

(2020) Sean P. Gordon et al.   Nature Communications

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

(2020) Shengchen Shan et al.   Frontiers in Genetics

Unbiased subgenome evolution in allotetraploid species of Ephedra and its implications for the evolution of large genomes in gymnosperms

(2020) Hui Wu et al.   Genome Biology and Evolution

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

(2020) Kevin A. Bird et al.   NEW PHYTOLOGIST

Unbiased subgenome evolution following a recent whole-genome duplication in pear (Pyrus bretschneideri Rehd.)

(2019) Qionghou Li et al.   Horticulture Research

Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)

(2019) Dmytro Kryvokhyzha et al.   PLoS Genetics

Origin and evolution of the octoploid strawberry genome

(2019) Patrick P. Edger et al.   NATURE GENETICS

The genome sequence of segmental allotetraploid peanut Arachis hypogaea

(2019) David J. Bertioli et al.   NATURE GENETICS

The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

(2019) Weijian Zhuang et al.   NATURE GENETICS

Breaking Free: the Genomics of Allopolyploidy-facilitated Niche Expansion in White Clover

(2019) Andrew G Griffiths et al.   PLANT CELL

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

CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis

(2019) Evan S Forsythe et al.   Genome Biology and Evolution

Extensive intraspecific gene order and gene structural variations in upland cotton cultivars

(2019) Zhaoen Yang et al.   Nature Communications

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

EAGLE: Explicit Alternative Genome Likelihood Evaluator

(2018) Tony Kuo et al.   BMC Medical Genomics

Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids

(2018) Ulrike Göbel et al.   Genome Biology and Evolution

Multiple large-scale gene and genome duplications during the evolution of hexapods

(2018) Zheng Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Expression Dominance in Allopolyploids: Hypotheses and Models

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

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

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

(2018) Jian Wu et al.   BMC GENOMICS

Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

(2018) Karl A. G. Kremling et al.   NATURE

The transcriptional landscape of polyploid wheat

(2018) R. H. Ramírez-González et al.   SCIENCE

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

(2018) Timothy Paape et al.   Nature Communications

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense

(2018) Maojun Wang et al.   NATURE GENETICS

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

The evolutionary significance of polyploidy

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

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

High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution

(2017) Artem S. Kasianov et al.   PLANT JOURNAL

Unstable Inheritance of 45S rRNA Genes in Arabidopsis thaliana

(2017) Fernando A. Rabanal et al.   G3-Genes Genomes Genetics

Updated taxonomic descriptions, iconography, and habitat preferences of Brachypodium distachyon, B. stacei, and B. hybridum (Poaceae)

(2016) Pilar Catalán et al.   ANALES DEL JARDIN BOTANICO DE MADRID

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

The challenge of evolving stable polyploidy: could an increase in “crossover interference distance” play a central role?

(2016) Kirsten Bomblies et al.   CHROMOSOMA

Genomic legacies of the progenitors and the evolutionary consequences of allopolyploidy

(2016) Kim A Steige et al.   CURRENT OPINION IN PLANT BIOLOGY

Ancient WGD events as drivers of key innovations in angiosperms

(2016) Pamela S Soltis et al.   CURRENT OPINION IN PLANT BIOLOGY

Nucleolar Dominance and Repression of 45S Ribosomal RNA Genes in Hybrids between Xenopus borealis and X. muelleri (2n = 36)

(2016) Sebastian Maciak et al.   CYTOGENETIC AND GENOME RESEARCH

PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq

(2016) Robert Kofler 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

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton

(2016) Jinlei Han et al.   PLANT JOURNAL

Experimental Evolution Reveals Interplay between Sch9 and Polyploid Stability in Yeast

(2016) Yi-Jin Lu et al.   PLoS Genetics

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

(2016) Tim Stuart et al.   eLife

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Transcriptome shock invokes disruption of parental expression-conserved genes in tetraploid wheat

(2016) Huakun Zhang et al.   Scientific Reports

Polyploidy and genome evolution in plants

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

Persistence of Subgenomes in Paleopolyploid Cotton after 60 My of Evolution

(2015) Simon Renny-Byfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

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

(2015) Xutong Wang et al.   NEW PHYTOLOGIST

Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

(2015) Vimal Rawat et al.   PLoS One

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploidCapsella bursa-pastoris

(2015) Gavin M. Douglas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome

(2015) Lunwen Qian et al.   BMC GENOMICS

Polyploidy in the Arabidopsis genus

(2014) Kirsten Bomblies et al.   CHROMOSOME RESEARCH

Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time

(2014) Gavin C Conant et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2014) Satoru Akama et al.   NUCLEIC ACIDS RESEARCH

Asymmetric Epigenetic Modification and Elimination of rDNA Sequences by Polyploidization in Wheat

(2014) Xiang Guo et al.   PLANT CELL

mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat

(2014) A. Li et al.   PLANT CELL

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

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

(2014) B. Chalhoub et al.   SCIENCE

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

(2014) Shengyi Liu et al.   Nature Communications

How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation

(2014) Vladimir V. Cavrak et al.   PLoS Genetics

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

(2014) Marc Bailly-Bechet et al.   Mobile DNA

Meiotic Adaptation to Genome Duplication in Arabidopsis arenosa

(2013) Levi Yant et al.   CURRENT BIOLOGY

Two Evolutionarily Distinct Classes of Paleopolyploidy

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

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

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

(2013) Tanja Slotte et al.   NATURE GENETICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat

(2013) Huakun Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Conservation and loss of ribosomal RNA gene sites in diploid and polyploid Fragaria (Rosaceae)

(2012) Bo Liu et al.   BMC PLANT BIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Homoeolog expression bias and expression level dominance in allopolyploid cotton

(2012) M-J Yoo et al.   HEREDITY

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

(2012) Beery Yaakov et al.   PLANT MOLECULAR BIOLOGY

Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa

(2012) Feng Cheng et al.   PLoS One

Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)

(2012) M. Chester et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa

(2012) Jesse D. Hollister et al.   PLoS Genetics

The more the better? The role of polyploidy in facilitating plant invasions

(2011) M. te Beest et al.   ANNALS OF BOTANY

The selfing syndrome: a model for studying the genetic and evolutionary basis of morphological adaptation in plants

(2011) Adrien Sicard et al.   ANNALS OF BOTANY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Immediate unidirectional epigenetic reprogramming of NORs occurs independently of rDNA rearrangements in synthetic and natural forms of a polyploid species Brassica napus

(2011) Tomasz Książczyk et al.   CHROMOSOMA

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

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

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Mutations in MYB3R1 and MYB3R4 Cause Pleiotropic Developmental Defects and Preferential Down-Regulation of Multiple G2/M-Specific Genes in Arabidopsis

(2011) N. Haga et al.   PLANT PHYSIOLOGY

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

Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus

(2011) Z. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners

(2011) Peter L Chang et al.   GENOME BIOLOGY

The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata

(2010) Steven Lockton et al.   BMC EVOLUTIONARY BIOLOGY

Nucleolar dominance and ribosomal RNA gene silencing

(2010) Sarah Tucker et al.   CURRENT OPINION IN CELL BIOLOGY

Genetic and Epigenetic Dynamics of a Retrotransposon After Allopolyploidization of Wheat

(2010) Z. Kraitshtein et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

The first meiosis of resynthesized Brassica napus, a genome blender

(2010) E. Szadkowski et al.   NEW PHYTOLOGIST

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

flowCore: a Bioconductor package for high throughput flow cytometry

(2009) Florian Hahne et al.   BMC BIOINFORMATICS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

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

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

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

(2009) Christian Parisod et al.   NEW PHYTOLOGIST

How to usefully compare homologous plant genes and chromosomes as DNA sequences

(2008) Eric Lyons et al.   PLANT JOURNAL

Genomic Plasticity and the Diversity of Polyploid Plants

(2008) A. R. Leitch et al.   SCIENCE

The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

(2008) Eric Lyons et al.   Tropical Plant Biology