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Considering founding and variable genomes is critical in studying polyploid evolution

https://doi.org/10.1101/738229
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Outgoing claims: the papers this work cites, builds on, or argues with.

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The Brassica napus Genome
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Effects of polyploidization on petal characteristics and optical properties of Impatiens walleriana (Hook.)
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Polyploidy and genome evolution in plants
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Polyploidy and genome evolution in plants
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Epigenetic and developmental regulation in plant polyploids
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Ancient WGD events as drivers of key innovations in angiosperms
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Wheat genomics comes of age
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Epigenetic perspectives on the evolution and domestication of polyploid plant and crops
inferredcites →https://doi.org/10.1016/j.pbi.2018.03.006openalex-snapshot
Subgenome assignment in allopolyploids: challenges and future directions
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Polyploidy: recurrent formation and genome evolution
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Genome evolution in polyploids
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Homoeolog expression bias and expression level dominance in allopolyploid cotton
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Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
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Ancestral polyploidy in seed plants and angiosperms
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Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
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Draft genome of the wheat A-genome progenitor Triticum urartu
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
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
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The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes
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Genome sequence of the cultivated cotton Gossypium arboreum
inferredcites →https://doi.org/10.1038/ng.3807openalex-snapshot
Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1038/nrg.2017.26openalex-snapshot
The evolutionary significance of polyploidy
inferredcites →https://doi.org/10.1038/s41467-019-09134-9openalex-snapshot
Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement
inferredcites →https://doi.org/10.1038/s41467-019-10757-1openalex-snapshot
Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus
inferredcites →https://doi.org/10.1038/s41467-019-12644-1openalex-snapshot
The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio
inferredcites →https://doi.org/10.1038/s41477-017-0096-3openalex-snapshot
Evolutionary dynamics of 3D genome architecture following polyploidization in cotton
inferredcites →https://doi.org/10.1038/s41477-018-0136-7openalex-snapshot
Gene retention, fractionation and subgenome differences in polyploid plants
inferredcites →https://doi.org/10.1038/srep18936openalex-snapshot
Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation
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Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat
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/10.1073/pnas.1934431100openalex-snapshot
Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates
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Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics
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Transport biofuels - a life-cycle assessment approach.
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Using transcriptomics to understand the wheat genome.
inferredcites →https://doi.org/10.1093/aob/mci078openalex-snapshot
Estimation of the Nuclear DNA Content of Gossypium Species
inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
inferredcites →https://doi.org/10.1093/genetics/147.3.1381openalex-snapshot
Rapid Elimination of Low-Copy DNA Sequences in Polyploid Wheat: A Possible Mechanism for Differentiation of Homoeologous Chromosomes
inferredcites →https://doi.org/10.1093/jxb/erv432openalex-snapshot
Whole genome duplications in plants: an overview fromArabidopsis
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The SWISS-PROT protein sequence data bank and its supplement TrEMBL
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The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998
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AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
inferredcites →https://doi.org/10.1101/gr.091678.109openalex-snapshot
Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
inferredcites →https://doi.org/10.1105/tpc.107.054346openalex-snapshot
Genomic Changes in Resynthesized Brassica napus and Their Effect on Gene Expression and Phenotype
inferredcites →https://doi.org/10.1105/tpc.114.124388openalex-snapshot
mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat
inferredcites →https://doi.org/10.1105/tpc.114.129841openalex-snapshot
Asymmetric Epigenetic Modification and Elimination of rDNA Sequences by Polyploidization in Wheat
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.1469-8137.2005.01347.xopenalex-snapshot
Ancient duplication of cereal 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.1469-8137.2012.04365.xopenalex-snapshot
Homoeolog expression bias and expression level dominance in allopolyploids
inferredcites →https://doi.org/10.1111/nph.13884openalex-snapshot
Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa
inferredcites →https://doi.org/10.1111/nph.14113openalex-snapshot
Reconciling the evolutionary origin of bread wheat (Triticum aestivum)
inferredcites →https://doi.org/10.1111/nph.15256openalex-snapshot
The causes and consequences of subgenome dominance in hybrids and recent polyploids
inferredcites →https://doi.org/10.1111/pbi.12651openalex-snapshot
The defence‐associated transcriptome of hexaploid wheat displays homoeolog expression and induction bias
inferredcites →https://doi.org/10.1111/tpj.12366openalex-snapshot
Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo‐ and neoduplicated subgenomes
inferredcites →https://doi.org/10.1111/tpj.13515openalex-snapshot
The pangenome of hexaploid bread wheat
inferredcites →https://doi.org/10.1111/tpj.13563openalex-snapshot
High‐quality genome assembly of Capsella bursa‐pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution
inferredcites →https://doi.org/10.1126/science.1251788openalex-snapshot
A chromosome-based draft sequence of the hexaploid bread wheat ( Triticum aestivum ) genome
inferredcites →https://doi.org/10.1126/science.1253435openalex-snapshot
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
inferredcites →https://doi.org/10.1126/science.aan0032openalex-snapshot
Wild emmer genome architecture and diversity elucidate wheat evolution and domestication
inferredcites →https://doi.org/10.1139/g01-011openalex-snapshot
Polyploid formation in cotton is not accompanied by rapid genomic changes
inferredcites →https://doi.org/10.1155/2018/9254302openalex-snapshot
Abundant Small Genetic Alterations after Upland Cotton Domestication
inferredcites →https://doi.org/10.1159/000313072openalex-snapshot
Development of Chromosome-Specific BAC Resources for Genomics of Bread Wheat
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-11-485openalex-snapshot
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
inferredcites →https://doi.org/10.1186/2047-217x-1-18openalex-snapshot
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
inferredcites →https://doi.org/10.1186/s12864-018-5357-7openalex-snapshot
A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication
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/10.1371/journal.pgen.1006012openalex-snapshot
DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton
inferredcites →https://doi.org/10.1371/journal.pone.0013708openalex-snapshot
Tissue-Specific Transcriptomics of the Exotic Invasive Insect Pest Emerald Ash Borer (Agrilus planipennis)
inferredcites →https://doi.org/10.1371/journal.pone.0081385openalex-snapshot
Chromosomal Characterization of the Three Subgenomes in the Polyploids of Hordeum murinum L.: New Insight into the Evolution of This Complex
inferredcites →https://doi.org/10.1534/genetics.104.034868openalex-snapshot
A Chromosome Bin Map of 16,000 Expressed Sequence Tag Loci and Distribution of Genes Among the Three Genomes of Polyploid Wheat
inferredcites →https://doi.org/10.1534/genetics.105.047894openalex-snapshot
Genomewide Nonadditive Gene Regulation in Arabidopsis Allotetraploids
inferredcites →https://doi.org/10.1534/genetics.112.146316openalex-snapshot
Genome Evolution Due to Allopolyploidization in Wheat
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