ArticleGenome research2006
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 234 papers.
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Who cites it
234 citing papers in PubMed, 466 citations in OpenAlex.
- Genome evolution through polyploidy: Enhancing plant stress resilience in agriculture.Proceedings of the National Academy of Sciences of the United States of America · 2026Review
- The evolution of gene expression in allopolyploid cotton relative to parental diploids and induced haploids.aBIOTECH · 2026Article
- Genome-Wide Analysis of the PEBP Gene Family and Functional Characterization ofInternational journal of molecular sciences · 2026Article
- Using genomic selection to examine subgenome dominance and epistasis in allopolyploid strawberry.The plant genome · 2026Article
- Subgenome Dominance in Allotetraploid Actinidia valvata Regulates RNA mAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- One versus many independent assemblies of symbiotic nitrogen fixation in flowering plants.Nature communications · 2025Review
- Effect of heterozygous deletions on phenotypic changes and dosage compensation in Arabidopsis thaliana.Scientific reports · 2025Article
- Whole Genome Duplication in the Genomics Era: The Hidden Gems in Invertebrates?Genome biology and evolution · 2025Review
- A chromosome-level genome assembly of the varied leaved jewelflower, Streptanthus diversifolius, reveals a recent whole genome duplication.G3 (Bethesda, Md.) · 2025Article
- A Class of Allopolyploidy Showing High Duplicate Retention and Continued Homoeologous Exchanges.Genome biology and evolution · 2025Article
- Repeated global adaptation across plant species.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Review
- 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
- The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.Nature genetics · 2024Article
- TheHorticulture research · 2024Article
- Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry.Nature communications · 2024Article
- Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression.PLoS computational biology · 2024Article
- Origin and evolution of the triploid cultivated banana genome.Nature genetics · 2024Article
- A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera.Communications biology · 2023Article
- Genome evolution and initial breeding of the Triticeae grassProceedings of the National Academy of Sciences of the United States of America · 2023Article
174 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Approximately 90% of Arabidopsis' unique gene content is found in syntenic blocks that were formed during the most recent whole-genome duplication. Within these blocks, 28.6% of the genes have a retained pair; the remaining genes have been lost from one of the homeologs. We create a minimized genome by condensing local duplications to one gene, removing transposons, and including only genes within blocks defined by retained pairs. We use a moving average of retained and non-retained genes to find clusters of retention and then identify the types of genes that appear in clusters at frequencies above expectations. Significant clusters of retention exist for almost all chromosomal segments. Detailed alignments show that, for 85% of the genome, one homeolog was preferentially (1.6x) targeted for fractionation. This homeolog fractionation bias suggests an epigenetic mechanism. We find that islands of retention contain "connected genes," those genes predicted-by the gene balance hypothesis-to be resistant to removal because the products they encode interact with other products in a dose-sensitive manner, creating a web of dependency. Gene families that are overrepresented in clusters include those encoding components of the proteasome/protein modification complexes, signal transduction machinery, ribosomes, and transcription factor complexes. Gene pair fractionation following polyploidy or segmental duplication leaves a genome enriched for "connected" genes. These clusters of duplicate genes may help explain the evolutionary origin of coregulated chromosomal regions and new functional modules.
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