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Background  The B3 DNA binding domain includes five families:  a uxin  r esponse  f actor (ARF),  a bscisic  a cid- i nsensitive 3  (ABI3),  h igh level expression of  s ugar  i nducible (HSI),  r elated to  A BI3/ V P1 (RAV) and  re productive  m eristem (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.    Methodology  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.

Evolution of the B3 DNA Binding Superfamily: New Insights into REM Family Gene Diversification