ArticleProceedings of the National Academy of Sciences of the United States of America2014
Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 104 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
104 citing papers in PubMed, 205 citations in OpenAlex.
- Contrasting regulation of protein-coding genes and lncRNA homeologs in allotetraploid Coffea arabica.Planta · 2026Article
- A fourth subgenome of the Camelina genus reveals gene dominance is influenced by chromosomal proximity.Nature communications · 2026Article
- High-Contiguity Haplotype-Resolved Genome Assembly of the Hexaploid Actinidia valvata Rootstock Sheds Light on Waterlogging Resistance Gene.Plant biotechnology journal · 2026Article
- Small RNAs regulation and genomic harmony: insights into allopolyploid evolution in marsh orchids (Dactylorhiza).The New phytologist · 2026Article
- Convergent subgenome dominance but with lineage-specific functional divergence of homoeologs during cave adaptation: insights from full-length transcriptomes of Sinocyclocheilus species.Frontiers in zoology · 2025Article
- Article
- A transposon insertion inHorticulture research · 2025Article
- Genome analyses and breeding of polyploid crops.Nature plants · 2025Review
- Subgenome Dominance in Allotetraploid Actinidia valvata Regulates RNA mAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome.Plants (Basel, Switzerland) · 2025Review
- Natural neopolyploids: a stimulus for novel research.The New phytologist · 2025Review
- Transgressive expression and dosage effect of A09 chromosome genes and their homoeologous genes influence the flowering time of resynthesized allopolyploid Brassica napus.BMC plant biology · 2025Article
- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- An improved transcriptome annotation reveals asymmetric expression and distinct regulation patterns in allotetraploid common carp.Communications biology · 2024Article
- Exploring genetic diversity, population structure, and subgenome differences in the allopolyploidHorticulture research · 2024Article
- Correlation Between Subgenome-biased DNA Loss and DNA Transposon Activation Following Hybridization in the Allotetraploid Xenopus Frogs.Genome biology and evolution · 2024Article
- Biased Retention of Environment-Responsive Genes Following Genome Fractionation.Molecular biology and evolution · 2024Article
- The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed.The plant genome · 2024Article
- Article
- Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression.PLoS computational biology · 2024Article
44 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome duplications happen repeatedly in a typical flowering plant lineage. Following most ancient tetraploidies, the two subgenomes are distinguishable because one subgenome, the dominant subgenome, tends to have more genes than the other subgenome. Additionally, among retained pairs, the gene on the dominant subgenome tends to be expressed more than its recessive homeolog. Using comparative genomics, we show that genome dominance is heritable. The dominant subgenome of one postpolyploidy event remains dominant through a subsequent polyploidy event. We show that transposon-derived 24-nt RNAs target and cover the upstream region of retained genes preferentially when located on the recessive subgenome, and with little regard for a gene's level of expression. We hypothesize that small RNA (smRNA)-mediated silencing of transposons near genes causes position-effect down-regulation. Unlike 24-nt smRNA coverage, transposon coverage tracks gene expression, so not all transposons behave identically. We propose that successful ancient tetraploids begin as wide crosses between two lines, each evolved for different tradeoffs between transposon silencing and negative position effects on gene expression. We hypothesize that following a chaotic wide-cross/new tetraploid period, genes acquire their new expression balances based on differences in transposon coverage in the parents. We envision patches of silenceable transposon as quantitative cis-regulators of baseline transcription rate. Attractive solutions to heterosis and the C-value paradox are mentioned.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.