ArticlePlant physiology2015
Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana.
Article in Plant physiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 45 citations in OpenAlex.
- Genome-wide in-silico characterization and expression pattern analysis of GATA transcription factor family in carrot (Daucus carota subsp. sativus).Functional & integrative genomics · 2026Article
- A natural variation within duplicated AsWRKY49-D2 drives the subgenomic functional divergence of homeologs in salt response of allohexaploid oats.Journal of integrative plant biology · 2026Article
- BnaCIPK9 homoeologs mediate the dosage-dependent regulation of seed oil in allotetraploid Brassica napus L.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Biased retention and functional diversification of CESA superfamily genes in Medicago mediating development and abiotic stress responses.BMC plant biology · 2026Article
- Metabolic and Molecular Rearrangements of Sauvignon Blanc (Plants (Basel, Switzerland) · 2023Article
- Genome-Wide Identification and Expression Profiles of C-Repeat Binding Factor Transcription Factors inInternational journal of molecular sciences · 2023Article
- Genome-wide identification and characterization of AP2/ERF gene superfamily during flower development in Actinidia eriantha.BMC genomics · 2022Article
- Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms inFrontiers in plant science · 2022Article
- The Breeding of Winter-Hardy Malting Barley.Plants (Basel, Switzerland) · 2021Review
- Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants.Molecular biology and evolution · 2020Article
- Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton.Nature communications · 2019Article
- Evolutionary dynamic analyses on monocot flavonoid 3'-hydroxylase gene family reveal evidence of plant-environment interaction.BMC plant biology · 2019Article
- Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication.BMC evolutionary biology · 2019Article
- Robust predictions of specialized metabolism genes through machine learning.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Angiosperm-Wide and Family-Level Analyses ofFrontiers in plant science · 2019Article
- Overexpression of Zinc Finger Transcription Factor ZAT6 Enhances Salt Tolerance.Open life sciences · 2018Article
- Transcriptomic changes reveal gene networks responding to the overexpression of a blueberry DWARF AND DELAYED FLOWERING 1 gene in transgenic blueberry plants.BMC plant biology · 2017Article
- Evolutionary and Functional Analysis of Membrane-Bound NAC Transcription Factor Genes in Soybean.Plant physiology · 2016Article
- Evolution of Gene Duplication in Plants.Plant physiology · 2016Review
- MYB31/MYB42 Syntelogs Exhibit Divergent Regulation of Phenylpropanoid Genes in Maize, Sorghum and Rice.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
Functional divergence between duplicate transcription factors (TFs) has been linked to critical events in the evolution of land plants and can result from changes in patterns of expression, binding site divergence, and/or interactions with other proteins. Although plant TFs tend to be retained post polyploidization, many are lost within tens to hundreds of million years. Thus, it can be hypothesized that some TFs in plant genomes are in the process of becoming pseudogenes. Here, we use a pair of salt tolerance-conferring transcription factors, DWARF AND DELAYED FLOWERING1 (DDF1) and DDF2, that duplicated through paleopolyploidy 50 to 65 million years ago, as examples to illustrate potential mechanisms leading to duplicate retention and loss. We found that the expression patterns of Arabidopsis thaliana (At)DDF1 and AtDDF2 have diverged in a highly asymmetric manner, and AtDDF2 has lost most inferred ancestral stress responses. Consistent with promoter disablement, the AtDDF2 promoter has fewer predicted cis-elements and a methylated repetitive element. Through comparisons of AtDDF1, AtDDF2, and their Arabidopsis lyrata orthologs, we identified significant differences in binding affinities and binding site preference. In particular, an AtDDF2-specific substitution within the DNA-binding domain significantly reduces binding affinity. Cross-species analyses indicate that both AtDDF1 and AtDDF2 are under selective constraint, but among A. thaliana accessions, AtDDF2 has a higher level of nonsynonymous nucleotide diversity compared with AtDDF1. This may be the result of selection in different environments or may point toward the possibility of ongoing functional decay despite retention for millions of years after gene duplication.
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