Abstract
The rapid alkalinization factor (RALF) gene family is essential for the plant growth and development. However, there is little known about these genes among Rosaceae species. Here, we identify 124 RALF-like genes from seven Rosaceae species, and 39 genes from Arabidopsis, totally 163 genes, divided into four clades according to the phylogenetic analysis, which includes 45 mature RALF genes from Rosaceae species. The YISY motif and RRXL cleavage site are typical features of true RALF genes, but some variants were detected in our study, such as YISP, YIST, NISY, YINY, YIGY, YVGY, FIGY, YIAY, and RRVM. Motif1 is widely distributed among all the clades. According to screening of cis-regulatory elements, GO annotation, expression sequence tags (EST), RNA-seq, and RT-qPCR, we reported that 24 RALF genes coding mature proteins related to tissue development, fungal infection, and hormone response. Purifying selection may play an important role in the evolutionary process of RALF-like genes among Rosaceae species according to the result from ka/ks. The tandem duplication event just occurs in four gene pairs (Fv-RALF9 and Fv-RALF10, Md-RALF7 and Md-RALF8, Pm-RALF2 and Pm-RALF8, and Pp-RALF11 and Pp-RALF14) from four Rosaceae species. Our research provides a wide overview of RALF-like genes in seven Rosaceae species involved in identification, classification, structure, expression, and evolution analysis.
Highlights
The rapid alkalinization factors (RALFs) belong to the small and cysteine-rich secreted peptides, which are involved in various processes of growth and development and play an important role in communication between cells in plants [1]
The genome-wide search for and verification of the seven Rosaceae species reference genomes indicated that there are 124 sequences with the RALF domain, with 41 from cultivated strawberry, 13 from wild strawberry, 20 from apple, nine from Japanese apricot, 17 from sweet cherry, 14 from peach, and 10 from European pear, in addition to 39 Arabidopsis RALF-like protein sequences that were retrieved from Phytozome [23] and previous research [4], among these 163 sequences, there are five common protein pairs
The majority of RALF-like proteins located extracellularly are involved in other positions, such as cell membrane, cytoplasm, endoplasmic reticulum, mitochondrion, and the nucleus, which implies these proteins mainly function outside the cell
Summary
The rapid alkalinization factors (RALFs) belong to the small and cysteine-rich secreted peptides, which are involved in various processes of growth and development and play an important role in communication between cells in plants [1]. Pearce et al [2] showed that mature peptides were almost 50 aa and contain four highly conserved cysteines in the C-terminus, which are essential for activation and are likely involved in disulfide bridges. Campbell and Turner [4] identified 765 RALF proteins from 51 plant species and divided them into four clades. There are typical features of RALFs in clades I, II, and III, including the RRXL cleavage site and the YISY motif. Clade IV lacks the typical RALF trait, whereas the members of clade IV exhibit diverse expression profiles and
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