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

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.

Keywords: GRF; gene duplication; gene structure; microsynteny; molecular evolution.

FIGURE 1

Chromosomal distribution and percentage share of GRF genes in pear, Populus, Arabidopsis, grape and Oryza sativa. The outermost ring represents chromosomes of pear, followed by Populus, grape, and Arabidopsis, and the innermost ring represents Oryza sativa.

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.

FIGURE 3

Exon-intron structure and motif compositions of GRF genes across five plant species. (A) Exon-intron structures of the GRF genes. Green rectangles: exons; thin lines: introns; blue boxes: untranslated regions (UTRs). (B) MEME motif search results. Note that different motifs are represented by different color boxes and that the length of each box does not show the true motif size.

FIGURE 4

Domain composition of GRFs. Fifty-eight GRFs have both the characteristic WRC and QLQ domains. The sequences of the QLQ and WRC domains of the 58 GRFs were aligned using ClustalW software to analyze their sequence features. These domain diagrams were plotted using the online WebLogo tool.

FIGURE 5

Extensive microsynteny of GRF regions across six plant species. The pear, apple, Populus, grape, Arabidopsis and rice chromosomes are depicted as different color boxes and labeled Pb, Md, Pt, Vv, At and Os, respectively. The scale on the circle is in megabases. Syntenic relationships between GRF regions are represented by black lines. The apple GRF gene family was obtained from The Apple Gene Function and Gene Family Database (Zhang et al., 2013).

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.

FIGURE 7

Scatter plots of the Ka/Ks ratios of duplicated GRF genes in pear, Populus, grape, Arabidopsis and rice. The X- and Y-axes denote the synonymous distance and Ka/Ks for each pair, respectively.

FIGURE 8

Sliding window plots of duplicated GRF genes in pear. The gray blocks, from light to dark, represent the positions of the WRC and QLQ domains, respectively. The window size is 150 bp, and the step size is 9 bp.