@ARTICLE{TreeBASE2Ref18868, author = {Daniel Lang and Benjamin Weiche and Gerrit Timmerhaus and Sandra Richardt and Diego M. Ria?o-Pach?n and Luiz G. G. Corr?a and Ralf Reski and Bernd Mueller-Roeber and Stefan A. Rensing}, title = {Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion and correlation with complexity}, year = {2010}, keywords = {transcription factor, evolution, Plantae, phylogenetic comparative methods, organism complexity}, doi = {10.1093/gbe/evq032}, url = {http://}, pmid = {}, journal = {Genome Biology and Evolution}, volume = {2}, number = {}, pages = {488--503}, 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 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 phylogenetic comparative 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 phylogenetic comparative 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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