title: High time for a roll call: gene duplication and phylogenetic relationships of TCP-like genes in monocots.
abstract: OBJECTIVE
  The TCP family is an ancient group of plant developmental transcription factors that regulate cell division in vegetative and reproductive structures and are essential in the establishment of flower zygomorphy. In-depth research on eudicot TCPs has documented their evolutionary and developmental role. This has not happened to the same extent in monocots, although zygomorphy has been critical for the diversification of Orchidaceae and Poaceae, the largest families of this group. Investigating the evolution and function of TCP-like genes in a wider group of monocots requires a detailed phylogenetic analysis of all available sequence information and a system that facilitates comparing genetic and functional information.
  
  
  METHODS
  The phylogenetic relationships of TCP-like genes in monocots were investigated by analysing sequences from the genomes of Zea mays, Brachypodium distachyon, Oryza sativa and Sorghum bicolor, as well as EST data from several other monocot species.
  
  
  RESULTS
  All available monocot TCP-like sequences are associated in 20 major groups with an average identity ≥64 % and most correspond to well-supported clades of the phylogeny. Their sequence motifs and relationships of orthology were documented and it was found that 67 % of the TCP-like genes of Sorghum, Oryza, Zea and Brachypodium are in microsyntenic regions. This analysis suggests that two rounds of whole genome duplication drove the expansion of TCP-like genes in these species.
  
  
  CONCLUSIONS
  A system of classification is proposed where putative or recognized monocot TCP-like genes are assigned to a specific clade of PCF-, CIN- or CYC/tb1-like genes. Specific biases in sequence data of this family that must be tackled when studying its molecular evolution and phylogeny are documented. Finally, the significant retention of duplicated TCP genes from Zea mays is considered in the context of balanced gene drive.
authors: Department of Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany. mariana.mondragon@biologie.uni-regensburg.de
authors: Mariana
authors: M
authors: Mondragón-Palomino
authors: Charlotte
authors: C
authors: Trontin
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D018076:DNA, Complementary; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D006109:Poaceae / Q000145:classification / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D018744:DNA, Plant; D010940:Plant Proteins; D018749:RNA, Plant; D014157:Transcription Factors