ArticleFrontiers in plant science2011
Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses.
Article in Frontiers in plant science, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 46 citations in OpenAlex.
- Lineage-specific evolution of regulatory landscapes in a polyploid plant and its diploid progenitors.bioRxiv : the preprint server for biology · 2026Article
- Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication.BMC biology · 2023Article
- Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms.Molecular biology and evolution · 2022Article
- Article
- Unbiased subgenome evolution following a recent whole-genome duplication in pear (Horticulture research · 2019Article
- Transcriptional and epigenetic adaptation of maize chromosomes in Oat-Maize addition lines.Nucleic acids research · 2018Article
- Article
- Article
- Evolutionary significance and diversification of the phosphoglucose isomerase genes in vertebrates.BMC research notes · 2015Article
- Gene expression and fractionation resistance.BMC genomics · 2014Article
- The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa.Genome biology and evolution · 2013Article
- Conserved Non-Coding Sequences are Associated with Rates of mRNA Decay in Arabidopsis.Frontiers in plant science · 2013Article
- High-resolution mapping of open chromatin in the rice genome.Genome research · 2012Article
- Escape from preferential retention following repeated whole genome duplications in plants.Frontiers in plant science · 2012Article
- Genome-wide analysis of syntenic gene deletion in the grasses.Genome biology and evolution · 2012Article
- Protein-Protein and Protein-DNA Dosage Balance and Differential Paralog Transcription Factor Retention in Polyploids.Frontiers in plant science · 2011Article
- Selection for higher gene copy number after different types of plant gene duplications.Genome biology and evolution · 2011Article
- Genome-wide patterns of homoeologous gene flow in allotetraploid coffee.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome duplications, or tetraploidies, are an important source of increased gene content. Following whole genome duplication, duplicate copies of many genes are lost from the genome. This loss of genes is biased both in the classes of genes deleted and the subgenome from which they are lost. Many or all classes are genes preferentially retained as duplicate copies are engaged in dose sensitive protein-protein interactions, such that deletion of any one duplicate upsets the status quo of subunit concentrations, and presumably lowers fitness as a result. Transcription factors are also preferentially retained following every whole genome duplications studied. This has been explained as a consequence of protein-protein interactions, just as for other highly retained classes of genes. We show that the quantity of conserved noncoding sequences (CNSs) associated with genes predicts the likelihood of their retention as duplicate pairs following whole genome duplication. As many CNSs likely represent binding sites for transcriptional regulators, we propose that the likelihood of gene retention following tetraploidy may also be influenced by dose-sensitive protein-DNA interactions between the regulatory regions of CNS-rich genes - nicknamed bigfoot genes - and the proteins that bind to them. Using grass genomes, we show that differential loss of CNSs from one member of a pair following the pre-grass tetraploidy reduces its chance of retention in the subsequent maize lineage tetraploidy.
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