Transcriptome and anatomical comparisons reveal the specific characteristics and genes involved in distinct types of growing culms

Moso bamboo can adopt both asexual and sexual reproduction strategies, which result in four main types of growing culms: bamboo shoots, seedling stems, leptomorph rhizomes and outward rhizomes. The genetic mechanisms underlying each type of growing culm remain elusive. Here, we performed comprehensive comparison of the four growing culms at the transcriptional and anatomical levels. Comparative transcriptome analyses showed that candidate genes in the photosynthesis pathway such as Lhca3 and PsbO were highly enriched in the seedling stems. The environmental response genes were highly expressed in outward rhizomes. Besides, genes related to cell cycle processes were predominantly transcribed in bamboo shoots, followed by rhizomes. The anatomical analyses indicated that cell division and elongation in rhizome internodes were only observed in the top section for a short period and barely in the middle and base of rhizome, which differentiate rhizome from other types of culms. In addition, observation on the phenotypic characteristics of winter bamboo shoots also indicated that winter period was important for primary thickening growth, energy storage, and node growth of bamboo shoots. Genes responsible for hormone signalling, cell cycle process, ARF and GRF transcription factors played important roles in this process. In situ hybridization, yeast two-hybrid screening and overexpression in rice indicated that two GRFs interacted with GIFs and played essential roles in moso bamboo shoot growth. In summary, the integration of comprehensive transcriptome profiling and anatomical analyses in this study have shed light on the molecular processes underlying different bamboo culms and provided valuable resources for future genetic research in moso bamboo.