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Background In plants, a critical balance between differentiation and proliferation of stem cells at the shoot apical meristem zone is essential for proper growth. The spatiotemporal regulation of some crucial genes dictates the formation of a boundary within and around budding organs. The boundary plays a pivotal role in distinguishing one tissue type from another and provides a defined shape to the organs at their developed stage. NAM/CUC subfamily of the NAC transcription factors control the boundary formation during meristematic development. Results Here, we have identified the  CUP-SHAPED COTYLEDON (CUC)  genes in sugarcane and named  SsCUC2  (for the orthologous gene of  CUC1  and  CUC2 ) and  SsCUC3 . The phylogenetic reconstruction showed that SsCUCs occupy the CUC2 and CUC3 clade together with monocots, whereas eudicot CUC2 and CUC3 settled separately in the different clade. The structural analysis of  CUC  genes showed that most of the  CUC3  genes were accompanied by an intron gain during eudicot divergence. Besides, the study of  SsCUC s expression in the RNA-seq obtained during different stages of ovule development revealed that  SsCUCs  express in developing young tissues, and the expression of  SsCUC2  is regulated by miR164. We also demonstrate that SsCUC2 (a monocot) could complement the  cuc2cuc3  mutant phenotype of  Arabidopsis  (eudicot). Conclusions This study further supports that  CUC2  has diverged in  CUC1  and  CUC2  during the evolution of monocots and eudicots from ancestral plants. The functional analysis of  CUC  expression patterns during sugarcane ovule development and ectopic expression of  SsCUC2  in  Arabidopsis  showed that SsCUC2 has a conserved role in boundary formation. Overall, these findings improve our understanding of the functions of sugarcane  CUC  genes. Our results reveal the crucial functional role of  CUC  genes in sugarcane.

Interspecific complementation-restoration of phenotype in Arabidopsis cuc2cuc3 mutant by sugarcane CUC2 gene