ArticleGenome biology2010
Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
36 citing papers in PubMed, 97 citations in OpenAlex.
- A comprehensive and accessible database of jawed-vertebrate ohnologs.Science advances · 2026Article
- Association of hybridization and genome doubling with codon usage landscapes in the subgenomes of bread wheat.Frontiers in plant science · 2026Article
- Comparative genomics, microsynteny, ancestral state reconstruction and selection pressure analysis across distinctive genomes and sub-genomes of Brassicaceae for analysis of evolutionary history ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2023Article
- Allelic expression ofFrontiers in plant science · 2023Article
- Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspecific hybridization.Functional & integrative genomics · 2022Article
- Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner.Plant methods · 2022Article
- Expression Level Dominance and Homeolog Expression Bias Upon Cold Stress in the F1 Hybrid Between the InvasiveFrontiers in genetics · 2022Article
- Expression Analysis ofFrontiers in plant science · 2022Article
- Spatial and Temporal Transcriptomic Heredity and Asymmetry in an Artificially Constructed Allotetraploid Wheat (AADD).Frontiers in plant science · 2022Article
- Gradual evolution of allopolyploidy in Arabidopsis suecica.Nature ecology & evolution · 2021Article
- Analysis of Transcriptional Changes in DifferentGenes · 2021Article
- An optimised chromatin immunoprecipitation (ChIP) method for starchy leaves of Nicotiana benthamiana to study histone modifications of an allotetraploid plant.Molecular biology reports · 2020Article
- Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors.Nature communications · 2020Article
- Homeolog expression quantification methods for allopolyploids.Briefings in bioinformatics · 2020Review
- Transcriptome Dynamics of the Inflorescence in Reciprocally Formed AllopolyploidFrontiers in genetics · 2020Article
- Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris).PLoS genetics · 2019Article
- A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids.Genetics · 2018Article
- Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.PLoS genetics · 2018Article
- Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica.Molecular biology and evolution · 2017Article
- The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection.Nature genetics · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAllotetraploids carry pairs of diverged homoeologs for most genes. With the genome doubled in size, the number of putative interactions is enormous. This poses challenges on how to coordinate the two disparate genomes, and creates opportunities by enhancing the phenotypic variation. New combinations of alleles co-adapt and respond to new environmental pressures. Three stages of the allopolyploidization process--parental species divergence, hybridization, and genome duplication--have been well analyzed. The last stage of evolutionary adjustments remains mysterious.
resultsHomoeolog-specific retention and use were analyzed in Arabidopsis suecica (As), a species derived from A. thaliana (At) and A. arenosa (Aa) in a single event 12,000 to 300,000 years ago. We used 405,466 diagnostic features on tiling microarrays to recognize At and Aa contributions to the As genome and transcriptome: 324 genes lacked Aa contributions and 614 genes lacked At contributions within As. In leaf tissues, 3,458 genes preferentially expressed At homoeologs while 4,150 favored Aa homoeologs. These patterns were validated with resequencing. Genes with preferential use of Aa homoeologs were enriched for expression functions, consistent with the dominance of Aa transcription. Heterologous networks--mixed from At and Aa transcripts--were underrepresented.
conclusionsThousands of deleted and silenced homoeologs in the genome of As were identified. Since heterologous networks may be compromised by interspecies incompatibilities, these networks evolve co-biases, expressing either only Aa or only At homoeologs. This progressive change towards predominantly pure parental networks might contribute to phenotypic variability and plasticity, and enable the species to exploit a larger range of environments.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.