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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.


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Microsynteny maps of GRF genes in Populus(A), grape (B), Arabidopsis(C), rice (D) and pear (E). The relative positions of all flanking protein-coding genes were defined by the anchored GRF genes, highlighted in red. Gray horizontal lines indicate the chromosome segments. Transcriptional orientations are represented by arrows. A gray line connects the conserved gene pairs among the segments.
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Figure 6: Microsynteny maps of GRF genes in Populus(A), grape (B), Arabidopsis(C), rice (D) and pear (E). The relative positions of all flanking protein-coding genes were defined by the anchored GRF genes, highlighted in red. Gray horizontal lines indicate the chromosome segments. Transcriptional orientations are represented by arrows. A gray line connects the conserved gene pairs among the segments.

Mentions: The pear genome contained nine GRF genes, eight of which (approximately 88.9%) were found in the duplication region of the genome (Figure 6E). In these gene pairs, six conserved genes were found in the flanking sequences of PbGRF02/PbGRF08; thus, this pair of genes was thought to have evolved from a large-scale duplication event. Nineteen GRF genes were included in the Populus genome, and 17 of these genes (approximately 89.5%) were found to be distributed on the duplicated segments of chromosomes (Figure 6A). As these genes (PtGRF03/PtGRF07, PtGRF05/PtGRF14, PtGRF05/PtGRF15, PtGRF04/PtGRF06, PtGRF11/PtGRF12, PtGRF11/PtGRF14, PtGRF12/PtGRF17, PtGRF13/PtGRF19, PtGRF14/PtGRF15, PtGRF08/PtGRF16) were located in high synteny regions (Figure 6A), their pairs were speculated to evolve from large-scale duplication events. In addition, the gene pair of PtGRF14 and PtGRF15 were located in the adjacent positions of chromosome 14 (Figure 6A), and therefore might be produced by tandem duplication. The Arabidopsis genome contained 9 GRF genes, four of which were found in the duplication regions of the genome. The flanking sequences of two gene pairs (AtGRF02/AtGRF08, AtGRF03/AtGRF06) had remarkable synteny (Figure 6C) and were inferred to have evolved from large-scale duplication events. Moreover, eight of 12 GRF genes were found in the duplication regions of the rice genome (Figure 6D). Conserved gene sequences were found in adjacent sequences of two gene pairs (OsGRF01/OsGRF06 and OsGRF02/OsGRF07), indicating that they were evolved from large-scale duplication events. In contrast, as OsGRF04 and OsGRF05 were located in adjacent positions on the same chromosome, the gene pair should be produced by tandem duplication. Only two of 8 GRF genes were found in the duplication regions of the grape genome. The synteny of the gene pair VvGRF03/VvGRF04 was weak in the duplicated region of the genome, and only two conserved genes were found on the flanking sequences (Figure 6B).


Comparative Genomic Analysis of the GRF Genes in Chinese Pear ( Pyrus bretschneideri Rehd ), Poplar ( Populous ), Grape ( Vitis vinifera ), Arabidopsis and Rice ( Oryza sativa )
Microsynteny maps of GRF genes in Populus(A), grape (B), Arabidopsis(C), rice (D) and pear (E). The relative positions of all flanking protein-coding genes were defined by the anchored GRF genes, highlighted in red. Gray horizontal lines indicate the chromosome segments. Transcriptional orientations are represented by arrows. A gray line connects the conserved gene pairs among the segments.
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Related In: Results  -  Collection

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Figure 6: Microsynteny maps of GRF genes in Populus(A), grape (B), Arabidopsis(C), rice (D) and pear (E). The relative positions of all flanking protein-coding genes were defined by the anchored GRF genes, highlighted in red. Gray horizontal lines indicate the chromosome segments. Transcriptional orientations are represented by arrows. A gray line connects the conserved gene pairs among the segments.
Mentions: The pear genome contained nine GRF genes, eight of which (approximately 88.9%) were found in the duplication region of the genome (Figure 6E). In these gene pairs, six conserved genes were found in the flanking sequences of PbGRF02/PbGRF08; thus, this pair of genes was thought to have evolved from a large-scale duplication event. Nineteen GRF genes were included in the Populus genome, and 17 of these genes (approximately 89.5%) were found to be distributed on the duplicated segments of chromosomes (Figure 6A). As these genes (PtGRF03/PtGRF07, PtGRF05/PtGRF14, PtGRF05/PtGRF15, PtGRF04/PtGRF06, PtGRF11/PtGRF12, PtGRF11/PtGRF14, PtGRF12/PtGRF17, PtGRF13/PtGRF19, PtGRF14/PtGRF15, PtGRF08/PtGRF16) were located in high synteny regions (Figure 6A), their pairs were speculated to evolve from large-scale duplication events. In addition, the gene pair of PtGRF14 and PtGRF15 were located in the adjacent positions of chromosome 14 (Figure 6A), and therefore might be produced by tandem duplication. The Arabidopsis genome contained 9 GRF genes, four of which were found in the duplication regions of the genome. The flanking sequences of two gene pairs (AtGRF02/AtGRF08, AtGRF03/AtGRF06) had remarkable synteny (Figure 6C) and were inferred to have evolved from large-scale duplication events. Moreover, eight of 12 GRF genes were found in the duplication regions of the rice genome (Figure 6D). Conserved gene sequences were found in adjacent sequences of two gene pairs (OsGRF01/OsGRF06 and OsGRF02/OsGRF07), indicating that they were evolved from large-scale duplication events. In contrast, as OsGRF04 and OsGRF05 were located in adjacent positions on the same chromosome, the gene pair should be produced by tandem duplication. Only two of 8 GRF genes were found in the duplication regions of the grape genome. The synteny of the gene pair VvGRF03/VvGRF04 was weak in the duplicated region of the genome, and only two conserved genes were found on the flanking sequences (Figure 6B).

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.


Related in: MedlinePlus