Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families.
BACKGROUND
Dof proteins are a family of plant-specific transcription factors that contain a particular class of zinc-finger DNA-binding domain. Members of this family have been found to play diverse roles in gene regulation of processes restricted to the plants. The completed genome sequences of rice and Arabidopsis constitute a valuable resource for comparative genomic analyses, since they are representatives of the two major evolutionary lineages within the angiosperms. In this framework, the identification of phylogenetic relationships among Dof proteins in these species is a fundamental step to unravel functionality of new and yet uncharacterised genes belonging to this group.


RESULTS
We identified 30 different Dof genes in the rice Oryza sativa genome and performed a phylogenetic analysis of a complete collection of the 36-reported Arabidopsis thaliana and the rice Dof transcription factors identified herein. This analysis led to a classification into four major clusters of orthologous genes and showed gene loss and duplication events in Arabidopsis and rice, that occurred before and after the last common ancestor of the two species.


CONCLUSIONS
According to our analysis, the Dof gene family in angiosperms is organized in four major clusters of orthologous genes or subfamilies. The proposed clusters of orthology and their further analysis suggest the existence of monocot specific genes and invite to explore their functionality in relation to the distinct physiological characteristics of these evolutionary groups.
Lijavetzky
Diego
D
Laboratorio de Bioquímica y Biología Molecular, Departamento de Biotecnología-UPM, E.T.S. Ingenieros Agrónomos, Ciudad Universitaria s/n, Madrid 28040, Spain. dlijavetzky@bit.etsia.upm.es
Carbonero
Pilar
P
Vicente-Carbajosa
Jesús
J
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant; D008969:Molecular Sequence Data; D005810:Multigene Family; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D017434:Protein Structure, Tertiary / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000235:genetics*; D016335:Zinc Fingers / Q000235:genetics
D029681:Arabidopsis Proteins; C407526:DAG1 protein, Arabidopsis; D004268:DNA-Binding Proteins; D010940:Plant Proteins; D014157:Transcription Factors