ArticleThe Plant journal : for cell and molecular biology2020
Phylogenomic analysis of the APETALA2 transcription factor subfamily across angiosperms reveals both deep conservation and lineage-specific patterns.
Article in The Plant journal : for cell and molecular biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed, 47 citations in OpenAlex.
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- Genome-Wide Superfamily Profiling Reveals Key RegulatorPlants (Basel, Switzerland) · 2026Article
- Article
- Evaluating the Combined Effects of Elevated [COPlant, cell & environment · 2026Article
- Phylogenomic Insights into High Conservation and Lineage-Specific Expansion of the ABAPT Gene Family in Plants.International journal of molecular sciences · 2026Article
- A PLETHORA3/7 transcription factor shapes cucumber shoot architecture.The New phytologist · 2026Article
- PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms.bioRxiv : the preprint server for biology · 2025Article
- Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development.Plant communications · 2025Article
- The AP2/ERF Gene Family in Camphor Tree: Structure, Evolution, and Transcriptional Response to Epicoccum Infection.Plants (Basel, Switzerland) · 2025Article
- Deciphering Plant NLR Genomic Evolution: Synteny-Informed Classification Unveils Insights into TNL Gene Loss.Molecular biology and evolution · 2025Article
- Phylogenomic analysis reveals exceptions to the co-evolution of ZAR1 and ZRK immune gene families in plants.BMC plant biology · 2025Article
- A computational Evo-Devo approach for elucidating the roles of PLETHORA transcription factors in regulating root development.PloS one · 2025Article
- APETALA2-like Floral Homeotic Protein Up-RegulatingInternational journal of molecular sciences · 2024Article
- PLETHORA transcription factors promote early embryo development through induction of meristematic potential.Development (Cambridge, England) · 2024Article
- Genome-wide analysis of AP2/ERF transcription factors that regulate fruit development of Chinese prickly ash.BMC plant biology · 2024Article
- Ancient Duplication and Lineage-Specific Transposition Determine Evolutionary Trajectory ofInternational journal of molecular sciences · 2024Article
- Exploring the evolution ofFrontiers in genetics · 2024Article
- Evolutionary dynamics and functional characterization of proximal duplicated sorbitol-6-phosphate dehydrogenase genes in Rosaceae.Frontiers in plant science · 2024Article
- Highly differentiated genomic properties underpin the different cell walls of Poaceae and eudicots.Plant physiology · 2023Article
- Syntenic Cell Wall QTLs as Versatile Breeding Tools: Intraspecific Allelic Variability and Predictability of Biomass Quality Loci in Target Plant Species.Plants (Basel, Switzerland) · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The APETALA2 (AP2) subfamily of transcription factors are key regulators of angiosperm root, shoot, flower and embryo development. The broad diversity of anatomical and morphological structures is potentially associated with the genomic dynamics of the AP2 subfamily. However, a comprehensive phylogenomic analysis of the AP2 subfamily across angiosperms is lacking. We combined phylogenetic and synteny analysis of distinct AP2 subclades in the completed genomes of 107 angiosperm species. We identified major changes in copy number variation and genomic context within subclades across lineages, and discuss how these changes may have contributed to the evolution of lineage-specific traits. Multiple AP2 subclades show highly conserved patterns of copy number and synteny across angiosperms, while others are more dynamic and show distinct lineage-specific patterns. As examples of lineage-specific morphological divergence due to AP2 subclade dynamics, we hypothesize that loss of PLETHORA1/2 in monocots correlates with the absence of taproots, whereas independent lineage-specific changes of PLETHORA4/BABY BOOM and WRINKLED1 genes in Brassicaceae and monocots point towards regulatory divergence of embryogenesis between these lineages. Additionally, copy number expansion of TOE1 and TOE3/AP2 in asterids is implicated with differential regulation of flower development. Moreover, we show that the genomic context of AP2s is in general highly specialized per angiosperm lineage. To our knowledge, this study is the first to shed light on the evolutionary divergence of the AP2 subfamily subclades across major angiosperm lineages and emphasizes the need for lineage-specific characterization of developmental networks to understand trait variability further.
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.