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Citation for Study 10409

Citation title: "Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion and correlation with complexity".

Study name: "Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion and correlation with complexity".

This study is part of submission 10399 (Status: Published).

Citation

Lang D., Weiche B., Timmerhaus G., Richardt S., Ria?o-pach?n D.M., Corr?a L.G., Reski R., Mueller-roeber B., & Rensing S.A. 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.

Authors

• Lang D. (submitter)
• Weiche B.
• Timmerhaus G.
• Richardt S.
• Ria?o-pach?n D.M.
• Corr?a L.G.
• Reski R.
• Mueller-roeber B.
• Rensing S.A.

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.

Keywords

transcription factor, evolution, Plantae, phylogenetic comparative methods, organism complexity

External links

• DOI: 10.1093/gbe/evq032

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10409
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@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.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 18868
  AU  - Lang,Daniel 
  AU  - Weiche,Benjamin 
  AU  - Timmerhaus,Gerrit 
  AU  - Richardt,Sandra 
  AU  - Ria?o-Pach?n,Diego  M.
  AU  - Corr?a,Luiz G. G. 
  AU  - Reski,Ralf 
  AU  - Mueller-Roeber,Bernd 
  AU  - Rensing,Stefan A.
  T1  - Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion and correlation with complexity
  PY  - 2010
  KW  - transcription factor
  KW  - evolution
  KW  - Plantae
  KW  - phylogenetic comparative methods
  KW  - organism complexity
  UR  - http://dx.doi.org/10.1093/gbe/evq032
  N2  - 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.
  L3  - 10.1093/gbe/evq032
  JF  - Genome Biology and Evolution
  VL  - 2
  IS  - 
  SP  - 488
  EP  - 503
  ER  -