title: Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity.
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.
authors.affiliation: Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Lang
authors.forename: Benjamin
authors.initials: B
authors.lastname: Weiche
authors.forename: Gerrit
authors.initials: G
authors.lastname: Timmerhaus
authors.forename: Sandra
authors.initials: S
authors.lastname: Richardt
authors.forename: Diego M
authors.initials: DM
authors.lastname: Riaño-Pachón
authors.forename: Luiz G G
authors.initials: LG
authors.lastname: Corrêa
authors.forename: Ralf
authors.initials: R
authors.lastname: Reski
authors.forename: Bernd
authors.initials: B
authors.lastname: Mueller-Roeber
authors.forename: Stefan A
authors.initials: SA
authors.lastname: Rensing
mesh_terms: D019143:Evolution, Molecular; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D008390:Markov Chains; D035683:MicroRNAs / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D010944:Plants / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics; D013997:Time Factors; D014157:Transcription Factors / Q000145:classification / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant; D014157:Transcription Factors