Journal Article

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

Daniel Lang, Benjamin Weiche, Gerrit Timmerhaus, Sandra Richardt, Diego M. Riaño-Pachón, Luiz G. G. Corrêa, Ralf Reski, Bernd Mueller-Roeber and Stefan A. Rensing

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 2, issue , pages 488-503
Published in print January 2010 |
Published online June 2010 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evq032

More Like This

Show all results sharing these subjects:

  • Bioinformatics and Computational Biology
  • Evolutionary Biology
  • Genetics and Genomics

GO

Show Summary Details

Preview

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.

Keywords: transcription factor; evolution; Plantae; phylogenetic comparative methods; morphological complexity

Journal Article.  9022 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.