ArticleGenome biology and evolution2010
Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity.
Article in Genome biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed, 188 citations in OpenAlex.
- PlantGATA: a comprehensive database for plant GATA transcription factors.Functional & integrative genomics · 2026Article
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- The secreted redox sensor roGFP2-Orp1 reveals oxidative dynamics in the plant apoplast.Plant biology (Stuttgart, Germany) · 2026Article
- Many transcription factor families have evolutionarily conserved binding motifs in plants.Plant physiology · 2025Article
- Evolution of sexual systems and regressive evolution in Riccia.The New phytologist · 2025Article
- Organismal complexity strongly correlates with the number of protein families and domains.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Enhanced sensitivity of TAPscan v4 enables comprehensive analysis of streptophyte transcription factor evolution.The Plant journal : for cell and molecular biology · 2025Article
- Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity.Nucleic acids research · 2024Article
- Fossil-calibrated molecular clock data enable reconstruction of steps leading to differentiated multicellularity and anisogamy in the Volvocine algae.BMC biology · 2024Article
- Genome-scale identification and comparative analysis of transcription factors in thermophilic cyanobacteria.BMC genomics · 2024Article
- Harnessing genetic engineering to drive economic bioproduct production in algae.Frontiers in bioengineering and biotechnology · 2024Review
- The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome.The Plant cell · 2022Article
- Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks.The plant genome · 2022Article
- Article
- Alternative splicing level related to intron size and organism complexity.BMC genomics · 2021Article
- Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.Genome biology and evolution · 2021Article
- Signatures of Transcription Factor Evolution and the Secondary Gain of Red Algae Complexity.Genes · 2021Article
- Gene-rich UV sex chromosomes harbor conserved regulators of sexual development.Science advances · 2021Article
- HAG1 and SWI3A/B control of male germ line development in P. patens suggests conservation of epigenetic reproductive control across land plants.Plant reproduction · 2021Article
- Role of epigenetics in unicellular to multicellular transition in Dictyostelium.Genome biology · 2021Article
26 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Evolutionary retention of duplicated genes encoding transcription-associated proteins (TAPs, comprising transcription factors and other transcriptional regulators) has been hypothesized to be positively correlated with increasing morphological complexity and paleopolyploidizations, especially within the plant kingdom. Here, we present the most comprehensive set of classification rules for TAPs and its application for genome-wide analyses of plants and algae. Using a dated species tree and phylogenetic comparative (PC) analyses, we define the timeline of TAP loss, gain, and expansion among Viridiplantae and find that two major bursts of gain/expansion occurred, coinciding with the water-to-land transition and the radiation of flowering plants. For the first time, we provide PC proof for the long-standing hypothesis that TAPs are major driving forces behind the evolution of morphological complexity, the latter in Plantae being shaped significantly by polyploidization and subsequent biased paleolog retention. Principal component analysis incorporating the number of TAPs per genome provides an alternate and significant proxy for complexity, ideally suited for PC genomics. Our work lays the ground for further interrogation of the shaping of gene regulatory networks underlying the evolution of organism complexity.
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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.