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Comparative Study
. 2010 Jul 19:2:488-503.
doi: 10.1093/gbe/evq032.

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

Daniel Lang  1 , Benjamin Weiche, Gerrit Timmerhaus, Sandra Richardt, Diego M Riaño-Pachón, Luiz G G Corrêa, Ralf Reski, Bernd Mueller-Roeber, Stefan A Rensing
Affiliations
Comparative Study

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

Daniel Lang et al. Genome Biol Evol. .

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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Figures

F<sc>IG</sc>. 1.—
FIG. 1.—
The sources of the TAP classification rules (supplementary table 1, Supplementary Material online) are depicted in a Venn diagram.
F<sc>IG</sc>. 2.—
FIG. 2.—
Visualization of the TAP classification rules (supplementary table 1, Supplementary Material online). Family names may contain blanks ( ), slashes (/), or dashes (-) as separation marks. Subfamily names are separated from the main family name by an underscore (_). See inset box for explanation of symbols.
F<sc>IG</sc>. 3.—
FIG. 3.—
(A) Absolute numbers of TAPs, subdivided as stacked bars depicting TFs (green), TRs (orange), and PTs (yellow), are shown per genome. Species abbreviations: see table 1. (B) Relative (percentage of total number of encoded proteins) amounts of TAPs, subdivided as stacked bars depicting TFs (green), TRs (orange), and PTs (yellow), are shown per genome. Species abbreviations: see table 1.
F<sc>IG</sc>. 4.—
FIG. 4.—
The PCA was performed on the absolute numbers of TAPs per family (uncorrected, phylogenetically dependent). A 2D plot of eigenitem 1 versus 2 is shown, with coloring according to taxonomic properties (blue: seed plants; red: nonseed plants; green: plastid derived from primary endosymbiosis; yellow: plastid derived from secondary endosymbiosis).
F<sc>IG</sc>. 5.—
FIG. 5.—
Extant and reconstructed ancestral numbers of TFs (green), TRs (orange), and PTs (yellow) per genome. Size of the boxes corresponds to the number of TAPs. The root used for the character tracing, C. merolae, was removed for brevity. The scale bar is in Ma.
See this image and copyright information in PMC

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