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.
Highlights
The results showed that the distribution of the 58 Growth-regulating factors (GRFs) genes among the chromosomes of the five species was not even (Figure 1)
GRF genes were distributed on chromosomes 1, 2, 3, 6, 7, 12, 13, 14, 15, 18, and 19
58 GRF gene members were analyzed, including their physical location, phylogenetic relationship, conserved microsynteny, gene duplication and Ka/Ks. These GRF genes were divided into five subfamilies
Summary
The first identified GRF, was rice OsGRF1 (van der Knaap et al, 2000). Subsequent studies found that GRF genes played a critical role in the regulation of plant growth and development (Kim et al, 2003; Horiguchi et al, 2005; Kuijt et al, 2014; Liang et al, 2014; Vercruyssen et al, 2015). The N-terminal of Arabidopsis GRF9 protein and Chinese cabbage GRF12 contain two WRC (Trp, Arg, Cys) structure domains (Kim et al, 2003; Wang et al, 2014), whereas the N-terminal of GRF proteins have one WRC and one QLQ (Gln, Leu, Gln) structure domain in the species studied (van der Knaap et al, 2000; Kim et al, 2003; Choi et al, 2004). The QLQ structure domain is similar to the N-terminal of SWI2/SNF2 in yeast, which could combine with SNF11 to form the chromatin remodeling complex
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