Multi-omics signatures of diverse plant callus cultures

Callus cultures are fundamental for plant propagation, genetic transformation, and emerging biotechnological applications that use cellular factories to produce high-value metabolites like plant-based drugs. These applications exploit the diverse metabolic capabilities of various plant species. However, optimizing culture conditions for specific applications necessitates a deep understanding of the transcriptome, metabolome, and phytohormone profiles of different species. Comprehensive comparative studies of callus characteristics across species are limited. Here, we analyzed the transcriptome, metabolome, and phytohormone profiles of callus cultures from tobacco (<i>Nicotiana tabacum</i>), rice (<i>Oryza sativa</i>), and two bamboo species (<i>Phyllostachys nigra</i> and <i>P. bambusoides</i>). Multivariate analyses of metabolome data revealed similar metabolic trends in these diverse callus cultures and identified metabolites that differ between species. Hormone profiling showed distinct species-specific patterns and notable cytokinin diversity, even between the bamboo species. Moreover, a comparative analysis of 8,256 pairs of syntenic genes between rice and bamboo revealed that 84.7% of these orthologs showed differential expression, indicating significant transcriptomic diversity despite phylogenomic relatedness. Transcriptional regulation of developing organs often involves conserved gene expression patterns across species; however, our findings suggest that callus formation may relax evolutionary constraints on these regulatory programs. These results illustrate the molecular diversity in callus cultures from multiple plant species, emphasizing the need to map this variability comprehensively to fully exploit the biotechnological potential of plant callus cultures.