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Comparative Genomic Analysis of the GRF Genes in Chinese Pear ( Pyrus bretschneideri Rehd ), Poplar ( Populous ), Grape ( Vitis vinifera ), Arabidopsis and Rice ( Oryza sativa )

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ABSTRACT

Growth-regulating factors (GRFs) are plant-specific transcription factors that have important functions in regulating plant growth and development. Previous studies on GRF family members focused either on a single or a small set of genes. Here, a comparative genomic analysis of the GRF gene family was performed in poplar (a model tree species), Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots), rice (a model plant for monocots) and Chinese pear (one of the economical fruit crops). In total, 58 GRF genes were identified, 12 genes in rice (Oryza sativa), 8 genes in grape (Vitis vinifera), 9 genes in Arabidopsis thaliana, 19 genes in poplar (Populus trichocarpa) and 10 genes in Chinese pear (Pyrus bretschneideri). The GRF genes were divided into five subfamilies based on the phylogenetic analysis, which was supported by their structural analysis. Furthermore, microsynteny analysis indicated that highly conserved regions of microsynteny were identified in all of the five species tested. And Ka/Ks analysis revealed that purifying selection plays an important role in the maintenance of GRF genes. Our results provide basic information on GRF genes in five plant species and lay the foundation for future research on the functions of these genes.

No MeSH data available.


Phylogenetic analysis of GRF genes in pear, Populus, Arabidopsis, grape and Oryza sativa. The species background for each GRF protein is represented by different colors. Based on the bootstrap values and evolutionary distances, the tree was clustered into five subfamilies. Gene names are listed in Supplementary Table S1. The scale bar represents 0.1 amino acid changes per site.
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Figure 2: Phylogenetic analysis of GRF genes in pear, Populus, Arabidopsis, grape and Oryza sativa. The species background for each GRF protein is represented by different colors. Based on the bootstrap values and evolutionary distances, the tree was clustered into five subfamilies. Gene names are listed in Supplementary Table S1. The scale bar represents 0.1 amino acid changes per site.

Mentions: Using the well-described GRF proteins in representative plant species, including the monocots Brachypodium distachyon, Oryza sativa, Setaria italic, Zea mays, Sorghum bicolor and the dicots Arabidopsis thaliana, Populus trichocarpa, Glycine max, Citrus sinensis, Vitis vinifera, Cucumis sativus, Brassica rapa and Chinese pear, the evolutionary relationships between members of the GRF families proteins were evaluated through phylogenetic analysis. According to the nodes of the phylogenetic tree, the NJ tree could be divided into five subfamilies, designated as I, II, III, IV, and V, respectively (Supplementary Figure S1). Subsequently, to further understand the similarity and evolutionary history of the GRF genes in rice, grape, Arabidopsis, Populus and Chinese pear, we built an unrooted phylogenetic tree using the NJ method in the MEGA7 software (Kumar et al., 2016). The NJ tree showed that 58 GRF proteins were divided into five subfamilies (Figure 2), which was consistent with the result from phylogenetic analysis (Supplementary Figure S1). The topology of these two phylogenetic trees and the distribution of GRF gene in each subfamily were basically the same (Figure 2; Supplementary Figure S1). Therefore, we focused our research on the evolution of the GRF family members in rice, grape, Arabidopsis, Populus and pear. As shown in Figure 2, subfamily III contained the minimal GRF numbers (2), and subfamily I has the maximal GRF numbers (21), followed by subfamily V (16) and subfamily IV (12). Each of the five species (rice, grape, Arabidopsis, Populus and pear) contributed at least one GRF gene to subfamily I, subfamily II and subfamily V, whereas, the members of subfamily III and subfamily IV included one, two or three species. Subfamily III consisted of only rice (monocots) and subfamily IV consisted of grape, Arabidopsis, Populus, and pear (dicots). Therefore, we deduced that this phenomenon may correspond to a special gene expansion event (lost or obtained) during the evolutionary process (Supplementary Figure S1; Figure 2). In addition, according to the phylogenetic tree (Figure 2), we identified pairs of orthologous genes among the GRF genes: PbGRF01 and PtGRF16, and PbGRF06 and VvGRF06, and PbGRF04 and PtGRF01.


Comparative Genomic Analysis of the GRF Genes in Chinese Pear ( Pyrus bretschneideri Rehd ), Poplar ( Populous ), Grape ( Vitis vinifera ), Arabidopsis and Rice ( Oryza sativa )
Phylogenetic analysis of GRF genes in pear, Populus, Arabidopsis, grape and Oryza sativa. The species background for each GRF protein is represented by different colors. Based on the bootstrap values and evolutionary distances, the tree was clustered into five subfamilies. Gene names are listed in Supplementary Table S1. The scale bar represents 0.1 amino acid changes per site.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC5121280&req=5

Figure 2: Phylogenetic analysis of GRF genes in pear, Populus, Arabidopsis, grape and Oryza sativa. The species background for each GRF protein is represented by different colors. Based on the bootstrap values and evolutionary distances, the tree was clustered into five subfamilies. Gene names are listed in Supplementary Table S1. The scale bar represents 0.1 amino acid changes per site.
Mentions: Using the well-described GRF proteins in representative plant species, including the monocots Brachypodium distachyon, Oryza sativa, Setaria italic, Zea mays, Sorghum bicolor and the dicots Arabidopsis thaliana, Populus trichocarpa, Glycine max, Citrus sinensis, Vitis vinifera, Cucumis sativus, Brassica rapa and Chinese pear, the evolutionary relationships between members of the GRF families proteins were evaluated through phylogenetic analysis. According to the nodes of the phylogenetic tree, the NJ tree could be divided into five subfamilies, designated as I, II, III, IV, and V, respectively (Supplementary Figure S1). Subsequently, to further understand the similarity and evolutionary history of the GRF genes in rice, grape, Arabidopsis, Populus and Chinese pear, we built an unrooted phylogenetic tree using the NJ method in the MEGA7 software (Kumar et al., 2016). The NJ tree showed that 58 GRF proteins were divided into five subfamilies (Figure 2), which was consistent with the result from phylogenetic analysis (Supplementary Figure S1). The topology of these two phylogenetic trees and the distribution of GRF gene in each subfamily were basically the same (Figure 2; Supplementary Figure S1). Therefore, we focused our research on the evolution of the GRF family members in rice, grape, Arabidopsis, Populus and pear. As shown in Figure 2, subfamily III contained the minimal GRF numbers (2), and subfamily I has the maximal GRF numbers (21), followed by subfamily V (16) and subfamily IV (12). Each of the five species (rice, grape, Arabidopsis, Populus and pear) contributed at least one GRF gene to subfamily I, subfamily II and subfamily V, whereas, the members of subfamily III and subfamily IV included one, two or three species. Subfamily III consisted of only rice (monocots) and subfamily IV consisted of grape, Arabidopsis, Populus, and pear (dicots). Therefore, we deduced that this phenomenon may correspond to a special gene expansion event (lost or obtained) during the evolutionary process (Supplementary Figure S1; Figure 2). In addition, according to the phylogenetic tree (Figure 2), we identified pairs of orthologous genes among the GRF genes: PbGRF01 and PtGRF16, and PbGRF06 and VvGRF06, and PbGRF04 and PtGRF01.

View Article: PubMed Central - PubMed

ABSTRACT

Growth-regulating factors (GRFs) are plant-specific transcription factors that have important functions in regulating plant growth and development. Previous studies on GRF family members focused either on a single or a small set of genes. Here, a comparative genomic analysis of the GRF gene family was performed in poplar (a model tree species), Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots), rice (a model plant for monocots) and Chinese pear (one of the economical fruit crops). In total, 58 GRF genes were identified, 12 genes in rice (Oryza sativa), 8 genes in grape (Vitis vinifera), 9 genes in Arabidopsis thaliana, 19 genes in poplar (Populus trichocarpa) and 10 genes in Chinese pear (Pyrus bretschneideri). The GRF genes were divided into five subfamilies based on the phylogenetic analysis, which was supported by their structural analysis. Furthermore, microsynteny analysis indicated that highly conserved regions of microsynteny were identified in all of the five species tested. And Ka/Ks analysis revealed that purifying selection plays an important role in the maintenance of GRF genes. Our results provide basic information on GRF genes in five plant species and lay the foundation for future research on the functions of these genes.

No MeSH data available.