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Divergence and adaptive evolution of the gibberellin oxidase genes in plants.

Huang Y, Wang X, Ge S, Rao GY - BMC Evol. Biol. (2015)

Bottom Line: On the basis of phylogenetic analyses and characteristic motifs of GAox genes, we demonstrated a rapid expansion and functional divergence of the GAox genes during the diversification of land plants.GAox genes originated very early-before the divergence of bryophytes and the vascular plants and the diversification of GAox genes is associated with the functional divergence and could be driven by positive selection.Our study not only provides information on the classification of GAox genes, but also facilitates the further functional characterization and analysis of GA oxidases.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Peking University, Beijing, 100871, China. huangyuan@pku.edu.cn.

ABSTRACT

Background: The important phytohormone gibberellins (GAs) play key roles in various developmental processes. GA oxidases (GAoxs) are critical enzymes in GA synthesis pathway, but their classification, evolutionary history and the forces driving the evolution of plant GAox genes remain poorly understood.

Results: This study provides the first large-scale evolutionary analysis of GAox genes in plants by using an extensive whole-genome dataset of 41 species, representing green algae, bryophytes, pteridophyte, and seed plants. We defined eight subfamilies under the GAox family, namely C19-GA2ox, C20-GA2ox, GA20ox,GA3ox, GAox-A, GAox-B, GAox-C and GAox-D. Of these, subfamilies GAox-A, GAox-B, GAox-C and GAox-D are described for the first time. On the basis of phylogenetic analyses and characteristic motifs of GAox genes, we demonstrated a rapid expansion and functional divergence of the GAox genes during the diversification of land plants. We also detected the subfamily-specific motifs and potential sites of some GAox genes, which might have evolved under positive selection.

Conclusions: GAox genes originated very early-before the divergence of bryophytes and the vascular plants and the diversification of GAox genes is associated with the functional divergence and could be driven by positive selection. Our study not only provides information on the classification of GAox genes, but also facilitates the further functional characterization and analysis of GA oxidases.

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Active site core of 2-oxoglutarate-dependent dioxygenases. Amino acid residues that bind the active-site Fe and those that interact with the 5-carboxylate of 2-oxoglutarate are highlighted in green and red, respectively. Six GAox homologs from algae are highlighted in blue
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Fig3: Active site core of 2-oxoglutarate-dependent dioxygenases. Amino acid residues that bind the active-site Fe and those that interact with the 5-carboxylate of 2-oxoglutarate are highlighted in green and red, respectively. Six GAox homologs from algae are highlighted in blue

Mentions: Our BLAST search results revealed 854 sequences of GAox homologs from the 41 species with whole genome sequencing data; these represent the main lineages of green plants (Additional file 2: Table S2). In algae, 6 putative GAox homologs were found based on the catalytic core amino acid sequences of 2OGDs in the carboxyl terminus (Fig. 3). As shown in Additional file 2: Table S2, the GAox genes varied across the different species and plant taxonomic groups, and there exist different distribution patterns for GAox subfamilies, especially for GAox-A, GAox-B, GAox-C and GAox-D. For instance, all 37 land plants have GAox gene homologs from the subfamilies C19-GA2ox, C20-GA2ox, GA20ox and GA3ox, while other subfamily genes are not present in one or more taxa, especially in some basal lineages of the land plants. In Physcomitrella patens genome, putative GAox homologs were only found in C19-GA2ox, GA3ox and GAox-C. There were no homologs of C20-GA2ox and GAox-B in a pteridophytes Selaginella moellendorffii. Homologs of C20-GA2ox and GA20ox were not found in a gymnosperm Picea abies. Of angiosperms, monocotyledons have all eight GAox subfamily homologs, while basal angiosperm Amborella trichopoda and some eudicotyledons have no GAox-D homologs in their genome. In addition, not only the distribution pattern but the gene sequence and structure were also varied between GAox genes of algae and land plants (Additional file 3: Data S1 and Additional file 4: Figure S1).Fig. 3


Divergence and adaptive evolution of the gibberellin oxidase genes in plants.

Huang Y, Wang X, Ge S, Rao GY - BMC Evol. Biol. (2015)

Active site core of 2-oxoglutarate-dependent dioxygenases. Amino acid residues that bind the active-site Fe and those that interact with the 5-carboxylate of 2-oxoglutarate are highlighted in green and red, respectively. Six GAox homologs from algae are highlighted in blue
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4587577&req=5

Fig3: Active site core of 2-oxoglutarate-dependent dioxygenases. Amino acid residues that bind the active-site Fe and those that interact with the 5-carboxylate of 2-oxoglutarate are highlighted in green and red, respectively. Six GAox homologs from algae are highlighted in blue
Mentions: Our BLAST search results revealed 854 sequences of GAox homologs from the 41 species with whole genome sequencing data; these represent the main lineages of green plants (Additional file 2: Table S2). In algae, 6 putative GAox homologs were found based on the catalytic core amino acid sequences of 2OGDs in the carboxyl terminus (Fig. 3). As shown in Additional file 2: Table S2, the GAox genes varied across the different species and plant taxonomic groups, and there exist different distribution patterns for GAox subfamilies, especially for GAox-A, GAox-B, GAox-C and GAox-D. For instance, all 37 land plants have GAox gene homologs from the subfamilies C19-GA2ox, C20-GA2ox, GA20ox and GA3ox, while other subfamily genes are not present in one or more taxa, especially in some basal lineages of the land plants. In Physcomitrella patens genome, putative GAox homologs were only found in C19-GA2ox, GA3ox and GAox-C. There were no homologs of C20-GA2ox and GAox-B in a pteridophytes Selaginella moellendorffii. Homologs of C20-GA2ox and GA20ox were not found in a gymnosperm Picea abies. Of angiosperms, monocotyledons have all eight GAox subfamily homologs, while basal angiosperm Amborella trichopoda and some eudicotyledons have no GAox-D homologs in their genome. In addition, not only the distribution pattern but the gene sequence and structure were also varied between GAox genes of algae and land plants (Additional file 3: Data S1 and Additional file 4: Figure S1).Fig. 3

Bottom Line: On the basis of phylogenetic analyses and characteristic motifs of GAox genes, we demonstrated a rapid expansion and functional divergence of the GAox genes during the diversification of land plants.GAox genes originated very early-before the divergence of bryophytes and the vascular plants and the diversification of GAox genes is associated with the functional divergence and could be driven by positive selection.Our study not only provides information on the classification of GAox genes, but also facilitates the further functional characterization and analysis of GA oxidases.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Peking University, Beijing, 100871, China. huangyuan@pku.edu.cn.

ABSTRACT

Background: The important phytohormone gibberellins (GAs) play key roles in various developmental processes. GA oxidases (GAoxs) are critical enzymes in GA synthesis pathway, but their classification, evolutionary history and the forces driving the evolution of plant GAox genes remain poorly understood.

Results: This study provides the first large-scale evolutionary analysis of GAox genes in plants by using an extensive whole-genome dataset of 41 species, representing green algae, bryophytes, pteridophyte, and seed plants. We defined eight subfamilies under the GAox family, namely C19-GA2ox, C20-GA2ox, GA20ox,GA3ox, GAox-A, GAox-B, GAox-C and GAox-D. Of these, subfamilies GAox-A, GAox-B, GAox-C and GAox-D are described for the first time. On the basis of phylogenetic analyses and characteristic motifs of GAox genes, we demonstrated a rapid expansion and functional divergence of the GAox genes during the diversification of land plants. We also detected the subfamily-specific motifs and potential sites of some GAox genes, which might have evolved under positive selection.

Conclusions: GAox genes originated very early-before the divergence of bryophytes and the vascular plants and the diversification of GAox genes is associated with the functional divergence and could be driven by positive selection. Our study not only provides information on the classification of GAox genes, but also facilitates the further functional characterization and analysis of GA oxidases.

Show MeSH