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An analytical framework for understanding regulatory novelty accompanying allopolyploidization

https://doi.org/10.1101/212092

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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

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Dominance and interloci interactions in transcriptional activation cascades: Models explaining compensatory mutations and inheritance patterns

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Epigenetic Variation Amongst Polyploidy Crop Species

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Physiology of Cotton

inferredcites →https://doi.org/10.1007/978-90-481-3195-2_1openalex-snapshot

The Origin and Evolution of Gossypium

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Faithful inheritance of cytosine methylation patterns in repeated sequences of the allotetraploid tobacco correlates with the expression of DNA methyltransferase gene families from both parental genomes

inferredcites →https://doi.org/10.1016/j.cell.2014.08.009openalex-snapshot

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

inferredcites →https://doi.org/10.1016/j.gde.2018.01.004openalex-snapshot

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

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Models of transcription factor binding: Sensitivity of activation functions to model assumptions

inferredcites →https://doi.org/10.1016/j.pbi.2012.01.015openalex-snapshot

Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants

inferredcites →https://doi.org/10.1016/j.pbi.2013.11.017openalex-snapshot

Epigenetics and plant genome evolution

inferredcites →https://doi.org/10.1016/j.pbi.2015.01.005openalex-snapshot

The ‘dark matter’ in the plant genomes: non-coding and unannotated DNA sequences associated with open chromatin

inferredcites →https://doi.org/10.1016/j.pbi.2016.02.006openalex-snapshot

Genomic legacies of the progenitors and the evolutionary consequences of allopolyploidy

inferredcites →https://doi.org/10.1016/j.pbi.2016.03.015openalex-snapshot

Ancient WGD events as drivers of key innovations in angiosperms

inferredcites →https://doi.org/10.1016/j.tplants.2017.06.003openalex-snapshot

Revisiting Pivotal-Differential Genome Evolution in Wheat

inferredcites →https://doi.org/10.1016/j.tplants.2018.01.002openalex-snapshot

Gene Expression Dominance in Allopolyploids: Hypotheses and Models

inferredcites →https://doi.org/10.1016/s0065-2113(02)78004-8openalex-snapshot

Polyploidy and the evolutionary history of cotton

inferredcites →https://doi.org/10.1038/459927aopenalex-snapshot

Unlocking the secrets of the genome

inferredcites →https://doi.org/10.1038/hdy.2009.182openalex-snapshot

Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species

inferredcites →https://doi.org/10.1038/hdy.2009.24openalex-snapshot

Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids

inferredcites →https://doi.org/10.1038/hdy.2012.79openalex-snapshot

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

inferredcites →https://doi.org/10.1038/hdy.2012.94openalex-snapshot

Homoeolog expression bias and expression level dominance in allopolyploid cotton

inferredcites →https://doi.org/10.1038/nature02698openalex-snapshot

Evolutionary changes in cis and trans gene regulation

inferredcites →https://doi.org/10.1038/nbt.3207openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ncomms1954openalex-snapshot

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

inferredcites →https://doi.org/10.1038/ncomms4930openalex-snapshot

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

inferredcites →https://doi.org/10.1038/ng.3657openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nprot.2017.055openalex-snapshot

Mapping genome-wide transcription-factor binding sites using DAP-seq

inferredcites →https://doi.org/10.1038/nrg.2017.26openalex-snapshot

The evolutionary significance of polyploidy

inferredcites →https://doi.org/10.1038/nrg2482openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nrg2600openalex-snapshot

The evolutionary significance of ancient genome duplications

inferredcites →https://doi.org/10.1038/s41598-017-02860-4openalex-snapshot

Gene-body CG methylation and divergent expression of duplicate genes in rice

inferredcites →https://doi.org/10.1038/srep44677openalex-snapshot

Chromatin modification contributes to the expression divergence of three TaGS2 homoeologs in hexaploid wheat

inferredcites →https://doi.org/10.1073/pnas.1000852107openalex-snapshot

Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana

inferredcites →https://doi.org/10.1073/pnas.1101368108openalex-snapshot

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

inferredcites →https://doi.org/10.1079/9780851999043.0000openalex-snapshot

Plant diversity and evolution: genotypic and phenotypic variation in higher plants

inferredcites →https://doi.org/10.1079/9780851999043.0097openalex-snapshot

Polyploidy and evolution in plants.

inferredcites →https://doi.org/10.1086/280872openalex-snapshot

The Significance of Polyploidy in Plant Evolution

inferredcites →https://doi.org/10.1086/284115openalex-snapshot

Polyploidy and Novelty in Flowering Plants

inferredcites →https://doi.org/10.1093/aob/mcn019openalex-snapshot

Evolution of rDNA in Nicotiana Allopolyploids: A Potential Link between rDNA Homogenization and Epigenetics

inferredcites →https://doi.org/10.1093/aob/mcp058openalex-snapshot

Phenotypic, genetic and genomic consequences of natural and synthetic polyploidization of Nicotiana attenuata and Nicotiana obtusifolia

inferredcites →https://doi.org/10.1093/gbe/evq038openalex-snapshot

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

inferredcites →https://doi.org/10.1093/gbe/evt072openalex-snapshot

RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations

inferredcites →https://doi.org/10.1093/gbe/evv057openalex-snapshot

Regulatory Divergence between Parental Alleles Determines Gene Expression Patterns in Hybrids

inferredcites →https://doi.org/10.1093/gbe/evw280openalex-snapshot

Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds

inferredcites →https://doi.org/10.1093/molbev/mst230openalex-snapshot

Two Evolutionarily Distinct Classes of Paleopolyploidy

inferredcites →https://doi.org/10.1093/molbev/msu085openalex-snapshot

Genome-Wide Disruption of Gene Expression in Allopolyploids but Not Hybrids of Rice Subspecies

inferredcites →https://doi.org/10.1093/molbev/msw096openalex-snapshot

The Footprint of Polygenic Adaptation on Stress-ResponsiveCis-Regulatory Divergence in theArabidopsis Genus

inferredcites →https://doi.org/10.1093/molbev/msx121openalex-snapshot

Gene Fractionation and Function in the Ancient Subgenomes of Maize

inferredcites →https://doi.org/10.1093/nar/gkt1376openalex-snapshot

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

inferredcites →https://doi.org/10.1093/nar/gkw1179openalex-snapshot

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

inferredcites →https://doi.org/10.1093/nar/gkw982openalex-snapshot

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

inferredcites →https://doi.org/10.1098/rspb.2009.1592openalex-snapshot

Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast

inferredcites →https://doi.org/10.1098/rspb.2014.2874openalex-snapshot

Genome reorganization in F 1 hybrids uncovers the role of retrotransposons in reproductive isolation

inferredcites →https://doi.org/10.1098/rstb.2013.0351openalex-snapshot

Polyploidy and novelty: Gottlieb's legacy

inferredcites →https://doi.org/10.1098/rstb.2013.0354openalex-snapshot

The legacy of diploid progenitors in allopolyploid gene expression patterns

inferredcites →https://doi.org/10.1101/gr.136184.111openalex-snapshot

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

inferredcites →https://doi.org/10.1104/pp.003095openalex-snapshot

Methylation and Phenotypic and Transcriptional Changes in Synthetic Arabidopsis Allotetraploids

inferredcites →https://doi.org/10.1105/tpc.107.052258openalex-snapshot

Allele-Specific Expression Patterns Reveal Biases and Embryo-Specific Parent-of-Origin Effects in Hybrid Maize

inferredcites →https://doi.org/10.1105/tpc.15.00911openalex-snapshot

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

inferredcites →https://doi.org/10.1105/tpc.17.00010openalex-snapshot

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

inferredcites →https://doi.org/10.1111/j.1365-294x.2005.02488.xopenalex-snapshot

Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae)

inferredcites →https://doi.org/10.1111/j.1469-8137.2005.01491.xopenalex-snapshot

Epigenetics and plant evolution

inferredcites →https://doi.org/10.1111/j.1469-8137.2009.03096.xopenalex-snapshot

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

inferredcites →https://doi.org/10.1111/j.1469-8137.2009.03107.xopenalex-snapshot

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

inferredcites →https://doi.org/10.1111/j.1469-8137.2010.03182.xopenalex-snapshot

The first meiosis of resynthesized Brassica napus, a genome blender

inferredcites →https://doi.org/10.1111/j.1469-8137.2010.03339.xopenalex-snapshot

Genome‐wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids

inferredcites →https://doi.org/10.1111/j.1469-8137.2011.03833.xopenalex-snapshot

Genomic expression dominance in the natural allopolyploid Coffea arabica is massively affected by growth temperature

inferredcites →https://doi.org/10.1111/j.1469-8137.2012.04365.xopenalex-snapshot

Homoeolog expression bias and expression level dominance in allopolyploids

inferredcites →https://doi.org/10.1111/mec.13626openalex-snapshot

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

inferredcites →https://doi.org/10.1111/mec.14297openalex-snapshot

Segmental allotetraploidy generates extensive homoeologous expression rewiring and phenotypic diversity at the population level in rice

inferredcites →https://doi.org/10.1111/nph.12108openalex-snapshot

Prevalence of gene expression additivity in genetically stable wheat allohexaploids

inferredcites →https://doi.org/10.1111/nph.12371openalex-snapshot

Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures

inferredcites →https://doi.org/10.1111/nph.13678openalex-snapshot

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

inferredcites →https://doi.org/10.1126/science.1153585openalex-snapshot

Genomic Plasticity and the Diversity of Polyploid Plants

inferredcites →https://doi.org/10.1126/science.1169766openalex-snapshot

A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation

inferredcites →https://doi.org/10.1126/science.1250091openalex-snapshot

Genome interplay in the grain transcriptome of hexaploid bread wheat

inferredcites →https://doi.org/10.1139/g08-006openalex-snapshot

Genetic and epigenetic changes of rDNA in a synthetic allotetraploid, Aegilops sharonensis × Ae. umbellulata

inferredcites →https://doi.org/10.1139/g09-004openalex-snapshot

Genome size in natural and synthetic autopolyploids and in a natural segmental allopolyploid of several Triticeae species

inferredcites →https://doi.org/10.1146/annurev-genet-120213-092159openalex-snapshot

Nonadditive Gene Expression in Polyploids

inferredcites →https://doi.org/10.1146/annurev-genet-120213-092443openalex-snapshot

pENCODE: A Plant Encyclopedia of DNA Elements

inferredcites →https://doi.org/10.1146/annurev.arplant.58.032806.103835openalex-snapshot

Genetic and Epigenetic Mechanisms for Gene Expression and Phenotypic Variation in Plant Polyploids

inferredcites →https://doi.org/10.1146/annurev.ecolsys.33.010802.150437openalex-snapshot

Neopolyploidy in Flowering Plants

inferredcites →https://doi.org/10.1186/1471-2164-11-505openalex-snapshot

Homoeolog-specific transcriptional bias in allopolyploid wheat

inferredcites →https://doi.org/10.1186/1471-2164-11-97openalex-snapshot

Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae)

inferredcites →https://doi.org/10.1186/1471-2229-14-3openalex-snapshot

Polyploidy and the petal transcriptome of Gossypium

inferredcites →https://doi.org/10.1186/1471-2229-9-80openalex-snapshot

On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae)

inferredcites →https://doi.org/10.1186/1741-7007-6-16openalex-snapshot

Duplicate gene expression in allopolyploid Gossypiumreveals two temporally distinct phases of expression evolution

inferredcites →https://doi.org/10.1186/1741-7007-7-18openalex-snapshot

Genomic expression dominance in allopolyploids

inferredcites →https://doi.org/10.1186/gb4051openalex-snapshot

Surveying the epigenomic landscape, one base at a time

inferredcites →https://doi.org/10.1186/s13059-017-1229-8openalex-snapshot

Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons

inferredcites →https://doi.org/10.1186/s13059-017-1254-7openalex-snapshot

Epigenomics: dissecting hybridization and polyploidization

inferredcites →https://doi.org/10.1371/journal.pbio.0040109openalex-snapshot

Functional Partitioning of Yeast Co-Expression Networks after Genome Duplication

inferredcites →https://doi.org/10.1371/journal.pgen.1004073openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pgen.1004180openalex-snapshot

An Interspecific Fungal Hybrid Reveals Cross-Kingdom Rules for Allopolyploid Gene Expression Patterns

inferredcites →https://doi.org/10.1371/journal.pgen.1004745openalex-snapshot

The Role of cis Regulatory Evolution in Maize Domestication

inferredcites →https://doi.org/10.1534/genetics.109.102608openalex-snapshot

Reciprocal Silencing, Transcriptional Bias and Functional Divergence of Homeologs in Polyploid Cotton (Gossypium)

inferredcites →https://doi.org/10.1534/genetics.111.127688openalex-snapshot

Extensive and Heritable Epigenetic Remodeling and Genetic Stability Accompany Allohexaploidization of Wheat

inferredcites →https://doi.org/10.2134/agronmonogr57.2013.0020openalex-snapshot

Taxonomy and Evolution of the Cotton Genus, Gossypium

inferredcites →https://doi.org/10.3389/fpls.2016.01508openalex-snapshot

Genome-Wide Gene Expressions Respond Differently to A-subgenome Origins in Brassica napus Synthetic Hybrids and Natural Allotetraploid

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.indcrop.2024.118552openalex-snapshot

Transgressive and subgenome expression level dominance and co-expression network analyses at the early fiber development in allopolyploid Gossypium

inferred← citeshttps://doi.org/10.1371/journal.pgen.1008131openalex-snapshot

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

inferred← citeshttps://doi.org/10.1640/0002-8444-109.3.224openalex-snapshot

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

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