Nanocarbons, such as fullerenes, carbon nanotubes, and graphene have attracted a great 11 deal of attention as next-generation materials because of their unprecedented structures and 12 unique physicochemical properties; however, almost all nanocarbons reported previously were 13 used as mixtures. Thus, there are still many unsolved issues about their biological functions at the 14 molecular level. Our synthetic campaign in the last decade has synthesized structurally uniform 15 and atomically precise nanocarbons, leading to the preparation of a library consisting of eighty 16 structurally diverse nanocarbon molecules. This resource motivated us to explore the as yet 17 uncovered biological functions of these nanocarbon molecules in organisms. Recently, nanotubes 18 were used to deliver genes to plants; however, the effects of the molecules on plants are not well 19 known. To monitor the effects of nanocarbon molecules on plants, we analyzed the transcriptome 20 of Arabidopsis thaliana seedlings treated with [9]cycloparaphenylene (CPP), decaborylated warped 21 nanographene (WNG), and dimethoxyhexabenzotetracene (HBT). Clustering analysis indicated 22 few effects of nanocarbon molecules on the transcriptome, perhaps suggesting a low toxicity of 23 nanocarbon molecules on plants. We found that AT1G05880 (ARIADNE 12) gene, categorized into 24 'response to hypoxia' genes, was up-regulated by nanocarbon molecules, suggesting that this gene 25 is usable as maker for treatment of nanocarbon molecules.26