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Energy cane is a dedicated crop to high biomass production and selected during Saccharum breeding programs to fit specific industrial needs for 2G bioethanol production. Internode elongation is one of the most important characteristics in Saccharum hybrids due to its relationship with crop yield. In this study, we selected the third internode elongation of the energy cane. To characterize this process, we divided the internode into five sections and performed a detailed transcriptome analysis (RNA-Seq) and cell wall characterization. The histological analyses revealed a remarkable gradient that spans from cell division and protoxylem lignification to the internode maturation and complete vascular bundle lignification. RNA-Seq analysis revealed more than 11,000 differentially expressed genes between the sections internal. Gene ontology analyzes showed enriched categories in each section, as well as the most expressed genes in each section, presented different biological processes. We found that the internode elongation and division zones have a large number of unique genes. Evaluated the specific profile of genes related to primary and secondary cell wall formation, cellulose synthesis, hemicellulose, lignin, and growth-related genes. For each section these genes presented different profiles along the internode in elongation in energy cane. The results of this study provide an overview of the regulation of gene expression of an internode elongation in energy cane. Gene expression analysis revealed promising candidates for transcriptional regulation of energy cane lignification and evidence key genes for the regulation of internode development, which can serve as a basis for understanding the molecular regulatory mechanisms that support the growth and development of plants in the Saccahrum complex.