Identification and comprehensive analysis of the CLV3/ESR-related (CLE) gene family in Brassica napus L.

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 analysis, which could facilitate the functional characterization of the peptides. Further characterization of CLE pre-propeptides revealed 31 unique CLE peptides from 45 BnCLE genes, which may give rise to distinct roles of BnCLEs and expansion of the gene family. The biological activity of these unique CLE dodecamer peptides was tested further through in vitro peptide assays. The variations of several important residues were identified as key contributors to the functional differentiation of BnCLEs and expansion of the gene family in B. napus. Expression profile analysis helped to characterize possible functional redundancy and sub-functionalization among the BnCLE members. This study presents a comprehensive overview of the CLE gene family in B. napus and provides a foundation for future evolutionary and functional studies.