The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity
Open accessAbstract
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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Citations
Cites
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793
Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906
Transcription regulation and animal diversity
Levine, M., & Tjian, R. (2003) · Nature · doi:10.1038/nature01763 · Cited by 1,309
The evolutionary significance of ancient genome duplications
Van de Peer, Y., Maere, S., & Meyer, A. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2600 · Cited by 1,129
A Molecular Timeline for the Origin of Photosynthetic Eukaryotes
Yoon, H. S., Hackett, J. D., Ciniglia, C., Pinto, G., & Bhattacharya, D. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh075 · Cited by 945
Evolution at Two Levels: On Genes and Form
Carroll, S. B. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030245 · Cited by 882
A molecular timescale of eukaryote evolution and the rise of complex multicellular life
Hedges, S. B., Blair, J. E., Venturi, M. L., & Shoe, J. L. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-2 · Cited by 578
Angiosperm diversification through time
Magallón, S., & Castillo, A. (2009) · American Journal of Botany · doi:10.3732/ajb.0800060 · Cited by 439
Protein Family Expansions and Biological Complexity
Vogel, C., & Chothia, C. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020048 · Cited by 227
The impact of fossils and taxon sampling on ancient molecular dating analyses
Hug, L. A., & Roger, A. J. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm115 · Cited by 144 · cited 4×
“…fossil constraints and protocols from the literature estimating CIs by averaging over time points obtained from multiple methods (supplementary table 6, Supplementary Material online; [Sanderson et al. 2004; Bell and Donoghue 2005; Hug and Roger 2007; Magallon and Castillo 2009; Wang et al. 2009]).”
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Cited by
One thousand plant transcriptomes and the phylogenomics of green plants
Initiative, O. T. P. T. (2019) · Nature · doi:10.1038/s41586-019-1693-2 · Cited by 1,734
The transcriptional landscape of polyploid wheat
Ramírez-González, R. H., Borrill, P., Lang, D., Harrington, S. A., Brinton, J., Venturini, L., Davey, M., Jacobs, J., van Ex, F., Pasha, A., et al. (2018) · Science · doi:10.1126/science.aar6089 · Cited by 1,018
Self-citationPlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
Jin, J., Zhang, H., Kong, L., Gao, G., & Luo, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1016 · Cited by 963
The Physcomitrella patens chromosome‐scale assembly reveals moss genome structure and evolution
Lang, D., Ullrich, K. K., Murat, F., Fuchs, J., Jenkins, J., Haas, F. B., Piednoel, M., Gundlach, H., Van Bel, M., Meyberg, R., et al. (2018) · The Plant Journal · doi:10.1111/tpj.13801 · Cited by 423
Self-citationThe hornwort genome and early land plant evolution
Zhang, J., Fu, X.-X., Li, R.-Q., Zhao, X., Liu, Y., Li, M.-H., Zwaenepoel, A., Ma, H., Goffinet, B., Guan, Y.-L., et al. (2020) · Nature Plants · doi:10.1038/s41477-019-0588-4 · Cited by 312
Metadata
- Authors
- Lang, D., Weiche, B., Timmerhaus, G., Richardt, S., Riaño-Pachón, D. M., Corrêa, L. G. G., Reski, R., Mueller-Roeber, B., & Rensing, S. A.
- Venue
- Genome Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-01-01
- Volume
- 2
- Pages
- 488-503
- ISSN
- 1759-6653 (ISSN-L)
- OpenAlex
- W2124924526
- Cited by
- 184
- References
- 10
- FWCI
- 11.64
- Type
- journal article
- Language
- en
- Open access
- gold
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