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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 ri...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2003
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC184357/ https://www.ncbi.nlm.nih.gov/pubmed/12877745 http://dx.doi.org/10.1186/1471-2148-3-17 |
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author | Lijavetzky, Diego Carbonero, Pilar Vicente-Carbajosa, Jesús |
author_facet | Lijavetzky, Diego Carbonero, Pilar Vicente-Carbajosa, Jesús |
author_sort | Lijavetzky, Diego |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-184357 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2003 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-1843572003-08-28 Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families Lijavetzky, Diego Carbonero, Pilar Vicente-Carbajosa, Jesús BMC Evol Biol Research Article 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. BioMed Central 2003-07-23 /pmc/articles/PMC184357/ /pubmed/12877745 http://dx.doi.org/10.1186/1471-2148-3-17 Text en Copyright © 2003 Lijavetzky et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. |
spellingShingle | Research Article Lijavetzky, Diego Carbonero, Pilar Vicente-Carbajosa, Jesús Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families |
title | Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families |
title_full | Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families |
title_fullStr | Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families |
title_full_unstemmed | Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families |
title_short | Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families |
title_sort | genome-wide comparative phylogenetic analysis of the rice and arabidopsis dof gene families |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC184357/ https://www.ncbi.nlm.nih.gov/pubmed/12877745 http://dx.doi.org/10.1186/1471-2148-3-17 |
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