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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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(A) Joined phylogenetic tree of the rice and Arabidopsis Dof gene families. The unrooted tree was inferred by the neighbor-joining method after the alignment of the Dof domain amino acid sequences of the 66 Arabidopsis and rice genes listed in Table 1 and 2 respectively. Arabidopsis (normal case) and rice genes (italics) are indicated at the end of solid and dotted branches, respectively. Bootstrapping values are indicated as percentages (when >50 %) along the branches. The resulting major clusters of orthologous genes (MCOG) are shown in different colors: Aa = orange, Bb = blue, Cc = red and Dd = green. Subscript numbers indicate the defined subgroups. The scale bar corresponds to 0.1 estimated amino acid substitution per site. Phylogenetic trees of rice (B) and Arabidopsis (C) Dof gene families. The unrooted trees were inferred by the neighbor-joining method after the alignment of the Dof domain amino acid sequences of the 30 rice and 36 Arabidopsis genes listed in Tables 1 and 2, respectively. The resulting groups are shown in different colors: A or a = orange, B or b = blue, C or c = red and D or d = green. Subscript numbers indicate the defined subgroups. The scale bar corresponds to 0.05 estimated amino acid substitutions per site. Genes belonging to the different groups are listed in Table 1 and 2.
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Figure 2: (A) Joined phylogenetic tree of the rice and Arabidopsis Dof gene families. The unrooted tree was inferred by the neighbor-joining method after the alignment of the Dof domain amino acid sequences of the 66 Arabidopsis and rice genes listed in Table 1 and 2 respectively. Arabidopsis (normal case) and rice genes (italics) are indicated at the end of solid and dotted branches, respectively. Bootstrapping values are indicated as percentages (when >50 %) along the branches. The resulting major clusters of orthologous genes (MCOG) are shown in different colors: Aa = orange, Bb = blue, Cc = red and Dd = green. Subscript numbers indicate the defined subgroups. The scale bar corresponds to 0.1 estimated amino acid substitution per site. Phylogenetic trees of rice (B) and Arabidopsis (C) Dof gene families. The unrooted trees were inferred by the neighbor-joining method after the alignment of the Dof domain amino acid sequences of the 30 rice and 36 Arabidopsis genes listed in Tables 1 and 2, respectively. The resulting groups are shown in different colors: A or a = orange, B or b = blue, C or c = red and D or d = green. Subscript numbers indicate the defined subgroups. The scale bar corresponds to 0.05 estimated amino acid substitutions per site. Genes belonging to the different groups are listed in Table 1 and 2.

Mentions: a Sequence name designation is arbitrary. b O. sativa ssp. japonica BAC/PAC clone name at the rice TIGR db. c O. sativa ssp. indica contig name at the NCBI O. sativa BLAST page. d Gene structure prediction according to the rice TIGR db (T) or to the RiceGAAS system (R). Intron (▼) relative position respect to the Dof domain. Sub-index indicates number of introns. e Chromosome assignment according to O. sativa ssp. japonica at the rice TIGR db. f Group designation after the phylogenetic analysis displayed in Figure 2B. g O. sativa ssp. japonica contig name at the rice TMRI db. h O. sativa ssp. japonica contig (at TMRI) containing incomplete gene (lacking the Dof domain) i O. sativa ssp. indica contig containing incomplete gene (lacking the Dof domain) j O. sativa ssp. indica contig containing a misassembled gene.


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

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

(A) Joined phylogenetic tree of the rice and Arabidopsis Dof gene families. The unrooted tree was inferred by the neighbor-joining method after the alignment of the Dof domain amino acid sequences of the 66 Arabidopsis and rice genes listed in Table 1 and 2 respectively. Arabidopsis (normal case) and rice genes (italics) are indicated at the end of solid and dotted branches, respectively. Bootstrapping values are indicated as percentages (when >50 %) along the branches. The resulting major clusters of orthologous genes (MCOG) are shown in different colors: Aa = orange, Bb = blue, Cc = red and Dd = green. Subscript numbers indicate the defined subgroups. The scale bar corresponds to 0.1 estimated amino acid substitution per site. Phylogenetic trees of rice (B) and Arabidopsis (C) Dof gene families. The unrooted trees were inferred by the neighbor-joining method after the alignment of the Dof domain amino acid sequences of the 30 rice and 36 Arabidopsis genes listed in Tables 1 and 2, respectively. The resulting groups are shown in different colors: A or a = orange, B or b = blue, C or c = red and D or d = green. Subscript numbers indicate the defined subgroups. The scale bar corresponds to 0.05 estimated amino acid substitutions per site. Genes belonging to the different groups are listed in Table 1 and 2.
© Copyright Policy
Related In: Results  -  Collection

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Figure 2: (A) Joined phylogenetic tree of the rice and Arabidopsis Dof gene families. The unrooted tree was inferred by the neighbor-joining method after the alignment of the Dof domain amino acid sequences of the 66 Arabidopsis and rice genes listed in Table 1 and 2 respectively. Arabidopsis (normal case) and rice genes (italics) are indicated at the end of solid and dotted branches, respectively. Bootstrapping values are indicated as percentages (when >50 %) along the branches. The resulting major clusters of orthologous genes (MCOG) are shown in different colors: Aa = orange, Bb = blue, Cc = red and Dd = green. Subscript numbers indicate the defined subgroups. The scale bar corresponds to 0.1 estimated amino acid substitution per site. Phylogenetic trees of rice (B) and Arabidopsis (C) Dof gene families. The unrooted trees were inferred by the neighbor-joining method after the alignment of the Dof domain amino acid sequences of the 30 rice and 36 Arabidopsis genes listed in Tables 1 and 2, respectively. The resulting groups are shown in different colors: A or a = orange, B or b = blue, C or c = red and D or d = green. Subscript numbers indicate the defined subgroups. The scale bar corresponds to 0.05 estimated amino acid substitutions per site. Genes belonging to the different groups are listed in Table 1 and 2.
Mentions: a Sequence name designation is arbitrary. b O. sativa ssp. japonica BAC/PAC clone name at the rice TIGR db. c O. sativa ssp. indica contig name at the NCBI O. sativa BLAST page. d Gene structure prediction according to the rice TIGR db (T) or to the RiceGAAS system (R). Intron (▼) relative position respect to the Dof domain. Sub-index indicates number of introns. e Chromosome assignment according to O. sativa ssp. japonica at the rice TIGR db. f Group designation after the phylogenetic analysis displayed in Figure 2B. g O. sativa ssp. japonica contig name at the rice TMRI db. h O. sativa ssp. japonica contig (at TMRI) containing incomplete gene (lacking the Dof domain) i O. sativa ssp. indica contig containing incomplete gene (lacking the Dof domain) j O. sativa ssp. indica contig containing a misassembled gene.

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