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Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families.

Lijavetzky D, Carbonero P, Vicente-Carbajosa J - BMC Evol. Biol. (2003)

Bottom Line: Members of this family have been found to play diverse roles in gene regulation of processes restricted to the plants.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: 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

ABSTRACT

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.

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Dof domain sequence alignment of the annotated rice proteins. The four cysteine residues putatively responsible of the zinc-finger structure are indicated. Identical amino acids are highlighted in black. Gene names correspond to those listed in Table 1.
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Figure 1: Dof domain sequence alignment of the annotated rice proteins. The four cysteine residues putatively responsible of the zinc-finger structure are indicated. Identical amino acids are highlighted in black. Gene names correspond to those listed in Table 1.

Mentions: In order to evaluate the evolutionary relationship among the rice Dof proteins, we performed a phylogenetic analysis based on their DNA binding domain sequences (Figure 1). Pair-wise amino acid similarities were higher than 50%, a threshold conventionally used to classify a group of genes as a gene family [5,37]. Consistent with the un-rooted tree obtained by the neighbor-joining algorithm (Figure 2B) four groups were defined (a, b, c and d), two of which were further divided into subgroups supported by the presence and position of introns (Table 1), bootstrapping values and the occurrence of common protein motifs outside of the Dof domain (Figure 3 and Table 3).


Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families.

Lijavetzky D, Carbonero P, Vicente-Carbajosa J - BMC Evol. Biol. (2003)

Dof domain sequence alignment of the annotated rice proteins. The four cysteine residues putatively responsible of the zinc-finger structure are indicated. Identical amino acids are highlighted in black. Gene names correspond to those listed in Table 1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC184357&req=5

Figure 1: Dof domain sequence alignment of the annotated rice proteins. The four cysteine residues putatively responsible of the zinc-finger structure are indicated. Identical amino acids are highlighted in black. Gene names correspond to those listed in Table 1.
Mentions: In order to evaluate the evolutionary relationship among the rice Dof proteins, we performed a phylogenetic analysis based on their DNA binding domain sequences (Figure 1). Pair-wise amino acid similarities were higher than 50%, a threshold conventionally used to classify a group of genes as a gene family [5,37]. Consistent with the un-rooted tree obtained by the neighbor-joining algorithm (Figure 2B) four groups were defined (a, b, c and d), two of which were further divided into subgroups supported by the presence and position of introns (Table 1), bootstrapping values and the occurrence of common protein motifs outside of the Dof domain (Figure 3 and Table 3).

Bottom Line: Members of this family have been found to play diverse roles in gene regulation of processes restricted to the plants.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: 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

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus