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Background   CLE  genes play various biological roles in plant growth and development, as well as in responses to environmental stimuli.    Results  In the present study, we identified nine  CLE  genes in the grape genome using an effective identification method. We analyzed the expression profiles of grape  CLE  genes in different tissues and under environmental different stimuli.  VvCLE3  was expressed in shoot apical meristem (SAM) enriched regions, and  VvCLE6  was expressed in shoot tissue without SAM. When grapes were infected with bois noir,  VvCLE2  was up-regulated. Under ABA treatment,  VvCLE3  was down-regulated.  VvCLE6  was up-regulated under high temperature stress. We found that  VvCLE6  and  VvCLE1  were highly expressed in root tissue. In addition, we compared the characteristics of CLEs from grape and other plant species. The CLE family in  Sphagnum fallax  underwent positive selection, while the CLE family in grape underwent purifying selection. The frequency of optimal codons and codon adaptation index of rice and grape CLE family members were positively correlated with GC content at the third site of synonymous codons, indicating that the dominant evolutionary pressure acting on rice and grape  CLE  genes was mutation pressure. We also found that closely related species had higher levels of similarity in relative synonymous codon usage in  CLE  genes. The rice  CLE  family was biased toward C and G nucleotides at third codon positions. Gene duplication and loss events were also found in grape  CLE  genes.    Conclusion  These results demonstrate an effective identification method for  CLE  motifs and increase the understanding of grape  CLEs . Future research on  CLE  genes may have applications for grape breeding and cultivation to better understand root and nodulation development.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5944-2) contains supplementary material, which is available to authorized users.

Genome-wide identification of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) family in grape (Vitis vinifera L.)