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The CLE (CLAVATA3/ESR) gene family, encoding a group of small secretory peptides, plays important roles in cell-to-cell communication, thereby controlling a broad spectrum of developmental processes. The CLE family has been systematically characterized in some plants but not Brassica napus. In the present study, 116 BnCLE genes were identified in the B. napus genome, including 7 unannotated, 6 incorrectly predicted and 5 multi-CLE domain-encoding genes. These BnCLE members were separated into seven distinct groups based on phylogenetic a