ArticlePlant physiology2006
Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication.
Article in Plant physiology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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96 citing papers in PubMed, 226 citations in OpenAlex.
- Dof Transcription Factors as Integrative Regulatory Hubs Linking Carbon-Nitrogen Metabolism, Development, and Environmental Signaling in Plants.Plant, cell & environment · 2026Review
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- Comprehensive analysis of SDH genes in Populus and functional characterization of SDH4 in xylem and cambium development.BMC plant biology · 2025Article
- Evolution and functional characterization of Populus salt stress-responsive calcineurin B-like protein-interacting protein kinases.Plant cell reports · 2024Article
- Genome-Wide Identification of theInternational journal of molecular sciences · 2024Article
- Identification and characterization of the Quinoa AP2/ERF gene family and their expression patterns in response to salt stress.Scientific reports · 2024Article
- Genome-Based Identification of the Dof Gene Family in ThreeInternational journal of molecular sciences · 2024Article
- Genome-Wide Characterization and Expression Profiling of the AP2/ERF Gene Family inInternational journal of molecular sciences · 2024Article
- Genome-wide in-silico analysis of ethylene biosynthesis gene family in Musa acuminata L. and their response under nutrient stress.Scientific reports · 2024Article
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- Superoxide dismutase gene family in cassava revealed their involvement in environmental stress via genome-wide analysis.iScience · 2023Article
- Genome-wide identification and characterization of SRLK gene family reveal their roles in self-incompatibility of Erigeron breviscapus.BMC genomics · 2023Article
- DOF transcription factors: Specific regulators of plant biological processes.Frontiers in plant science · 2023Review
- Genome-wide identification ofPeerJ · 2023Article
- Transcriptomic Evidence Reveals Low Gelatinous Layer Biosynthesis inInternational journal of molecular sciences · 2022Article
- Genome-wide identification and functional analysis of Dof transcription factor family in Camelina sativa.BMC genomics · 2022Article
- Tubby-like proteins (TLPs) transcription factor in different regulatory mechanism in plants: a review.Plant molecular biology · 2022Review
- Genome-Wide Identification of AP2/ERF Transcription Factor Family and Functional Analysis ofInternational journal of molecular sciences · 2022Article
- Ectopic Expression ofInternational journal of molecular sciences · 2022Article
36 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is widely accepted that gene duplication is a primary source of genetic novelty. However, the evolutionary fate of duplicated genes remains largely unresolved. The classical Ohno's Duplication-Retention-Non/Neofunctionalization theory, and the recently proposed alternatives such as subfunctionalization or duplication-degeneration-complementation, and subneofunctionalization, each can explain one or more aspects of gene fate after duplication. Duplicated genes are also affected by epigenetic changes. We constructed a phylogenetic tree using Dof (DNA binding with one finger) protein sequences from poplar (Populus trichocarpa) Torr. & Gray ex Brayshaw, Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa). From the phylogenetic tree, we identified 27 pairs of paralogous Dof genes in the terminal nodes. Analysis of protein motif structure of the Dof paralogs and their ancestors revealed six different gene fates after gene duplication. Differential protein methylation was revealed between a pair of duplicated poplar Dof genes, which have identical motif structure and similar expression pattern, indicating that epigenetics is involved in evolution. Analysis of reverse transcription-PCR, massively parallel signature sequencing, and microarray data revealed that the paralogs differ in expression pattern. Furthermore, analysis of nonsynonymous and synonymous substitution rates indicated that divergence of the duplicated genes was driven by positive selection. About one-half of the motifs in Dof proteins were shared by non-Dof proteins in the three plants species, indicating that motif co-option may be one of the forces driving gene diversification. We provided evidence that the Ohno's Duplication-Retention-Non/Neofunctionalization, subfunctionalization/duplication-degeneration-complementation, and subneofunctionalization hypotheses are complementary with, not alternative to, each other.
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