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  Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity

Lang, D., Weiche, B., Timmerhaus, G., Richardt, S., Riano-Pachon, D. M., Correa, L. G. G., et al. (2010). Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity. Genome Biology and Evolution, 2, 488-503. doi:10.1093/gbe/evq032.

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 Creators:
Lang, D.1, Author
Weiche, B.1, Author
Timmerhaus, G.1, Author
Richardt, S.1, Author
Riano-Pachon, D. M.2, Author           
Correa, L. G. G.3, Author           
Reski, R.1, Author
Mueller-Roeber, B.3, Author           
Rensing, S. A.1, Author
Affiliations:
1External Organizations, ou_persistent22              
2BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753315              
3Plant Signalling, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753311              

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Free keywords: transcription factor evolution plantae phylogenetic comparative methods morphological complexity multiple sequence alignment morphological complexity factor database gene family divergence times molecular clock early evolution volvox-carteri arabidopsis protein
 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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Language(s): eng - English
 Dates: 2010-07-212010
 Publication Status: Issued
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 Identifiers: ISI: ISI:000280480000042
DOI: 10.1093/gbe/evq032
ISSN: 1759-6653 (Electronic)
URI: ://000280480000042 http://gbe.oxfordjournals.org/content/2/488.full.pdf
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Title: Genome Biology and Evolution
Source Genre: Journal
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Pages: - Volume / Issue: 2 Sequence Number: - Start / End Page: 488 - 503 Identifier: -