title: The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling.
abstract: BACKGROUND
  Transcription factors (TFs) are proteins that have played a central role both in evolution and in domestication, and are major regulators of development in living organisms. Plant genome sequences reveal that approximately 7% of all genes encode putative TFs. The DOF (DNA binding with One Finger) TF family has been associated with vital processes exclusive to higher plants and to their close ancestors (algae, mosses and ferns). These are seed maturation and germination, light-mediated regulation, phytohormone and plant responses to biotic and abiotic stresses, etc. In Hordeum vulgare and Oryza sativa, 26 and 30 different Dof genes, respectively, have been annotated. Brachypodium distachyon has been the first Pooideae grass to be sequenced and, due to its genomic, morphological and physiological characteristics, has emerged as the model system for temperate cereals, such as wheat and barley.
  
  
  RESULTS
  Through searches in the B. distachyon genome, 27 Dof genes have been identified and a phylogenetic comparison with the Oryza sativa and the Hordeum vulgare DOFs has been performed. To explore the evolutionary relationship among these DOF proteins, a combined phylogenetic tree has been constructed with the Brachypodium DOFs and those from rice and barley. This phylogenetic analysis has classified the DOF proteins into four Major Cluster of Orthologous Groups (MCOGs). Using RT-qPCR analysis the expression profiles of the annotated BdDof genes across four organs (leaves, roots, spikes and seeds) has been investigated. These results have led to a classification of the BdDof genes into two groups, according to their expression levels. The genes highly or preferentially expressed in seeds have been subjected to a more detailed expression analysis (maturation, dry stage and germination).
  
  
  CONCLUSIONS
  Comparison of the expression profiles of the Brachypodium Dof genes with the published functions of closely related DOF sequences from the cereal species considered here, deduced from the phylogenetic analysis, indicates that although the expression profile has been conserved in many of the putative orthologs, in some cases duplication followed by subsequent divergence may have occurred (neo-functionalization).
authors.affiliation: Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain.
authors.forename: Sara
authors.initials: S
authors.lastname: Hernando-Amado
authors.forename: Virginia
authors.initials: V
authors.lastname: González-Calle
authors.forename: Pilar
authors.initials: P
authors.lastname: Carbonero
authors.forename: Cristina
authors.initials: C
authors.lastname: Barrero-Sicilia
mesh_terms: D058431:Brachypodium / Q000235:genetics*; D017124:Conserved Sequence; D018745:Genome, Plant; D018525:Germination / Q000235:genetics; D001467:Hordeum / Q000235:genetics; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D012639:Seeds / Q000235:genetics; D016415:Sequence Alignment; D014157:Transcription Factors / Q000145:classification / Q000235:genetics*; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant; D014157:Transcription Factors