title: Evolution of the B3 DNA binding superfamily: new insights into REM family gene diversification.
abstract: BACKGROUND
  The B3 DNA binding domain includes five families: auxin response factor (ARF), abscisic acid-insensitive3 (ABI3), high level expression of sugar inducible (HSI), related to ABI3/VP1 (RAV) and reproductive meristem (REM). The release of the complete genomes of the angiosperm eudicots Arabidopsis thaliana and Populus trichocarpa, the monocot Orysa sativa, the bryophyte Physcomitrella patens,the green algae Chlamydomonas reinhardtii and Volvox carteri and the red algae Cyanidioschyzon melorae provided an exceptional opportunity to study the evolution of this superfamily.
  
  
  METHODS
  In order to better understand the origin and the diversification of B3 domains in plants, we combined comparative phylogenetic analysis with exon/intron structure and duplication events. In addition, we investigated the conservation and divergence of the B3 domain during the origin and evolution of each family.
  
  
  CONCLUSIONS
  Our data indicate that showed that the B3 containing genes have undergone extensive duplication events, and that the REM family B3 domain has a highly diverged DNA binding. Our results also indicate that the founding member of the B3 gene family is likely to be similar to the ABI3/HSI genes found in C. reinhardtii and V. carteri. Among the B3 families, ABI3, HSI, RAV and ARF are most structurally conserved, whereas the REM family has experienced a rapid divergence. These results are discussed in light of their functional and evolutionary roles in plant development.
authors.affiliation: Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Elisson A C
authors.initials: EA
authors.lastname: Romanel
authors.forename: Carlos G
authors.initials: CG
authors.lastname: Schrago
authors.forename: Rafael M
authors.initials: RM
authors.lastname: Couñago
authors.forename: Claudia A M
authors.initials: CA
authors.lastname: Russo
authors.forename: Márcio
authors.initials: M
authors.lastname: Alves-Ferreira
mesh_terms: D017360:Arabidopsis / Q000737:chemistry / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics*; D005075:Biological Evolution; D056890:Eukaryota / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D018521:Plant Physiological Phenomena; D010940:Plant Proteins; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D003313:Zea mays / Q000737:chemistry / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D010940:Plant Proteins