The N⁶-methyladenosine (m⁶A) methylation of mRNA is involved in biological processes essential for plant growth. To explore the m⁶A modification of sugarcane and reveal its regulatory function, methylated RNA immunoprecipitation sequencing (MeRIP-seq) was used to construct the m⁶A map of sugarcane. In this study, m⁶A sites of sugarcane transcriptome were significantly enriched around the stop codon and within 3′-untranslated regions (3′UTR). Gene ontology (GO) analysis showed that the m⁶A modification genes are associated with metabolic biosynthesis. In addition, the m⁶A modification of drought-resistant transcript mRNA increased significantly under drought (DR) treatment, resulting in enhanced mRNA stability, which is involved in regulating sugarcane drought resistance. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results showed that differentially methylated peak (DMP) modification of differentially expressed genes (DEGs) in DR were particularly associated with abscisic acid (ABA) biosynthesis. The upregulated genes were significantly enriched in the ABA metabolism, ethylene response, fatty acid metabolism, and negative regulation of the abscisic acid activation signaling pathway. These findings provide a basis and resource for sugarcane RNA epigenetic studies and further increase our knowledge of the functions of m⁶A modifications in RNA under abiotic stress.

Sugarcane is an important crop across the globe, and the rapid multiplication of excellent cultivars is an important object of the sugarcane industry. As one of the plant growth regulators, paclobutrazol (PBZ) has been frequently used in the tissue culture of sugarcane seedlings. However, little is known about the molecular mechanisms of response to PBZ in this crop. Here, we performed a comparative transcriptome analysis between sensitive (LC05−136) and non−sensitive (GGZ001) sugarcane cultivars treated by PBZ at three time points (0 d, 10 d, and 30 d) using RNA sequencing (RNA−Seq). The results showed that approximately 70.36 Mb of clean data for each sample were generated and assembled into 239,212 unigenes. A total of 6108 and 4404 differentially expressed genes (DEGs) were identified within the sensitive and non−sensitive sugarcane cultivars, respectively. Among them, DEGs in LC05−136 were most significantly enriched in the photosynthesis and valine, leucine and isoleucine degradation pathways, while in GGZ001, DEGs associated with ion channels and plant–pathogen interaction were mainly observed. Notably, many interesting genes, including those encoding putative regulators, key components of photosynthesis, amino acids degradation and glutamatergic synapse, were identified, revealing their importance in the response of sugarcane to PBZ. Furthermore, the expressions of sixteen selected DEGs were tested by quantitative reverse transcription PCR (RT−qPCR), confirming the reliability of the RNA−seq data used in this study. These results provide valuable information regarding the transcriptome changes in sugarcane treated by PBZ and provide an insight into understanding the molecular mechanisms underlying the resistance to PBZ in sugarcane.

Furanocoumarins and their derivatives are found in various plant species and have attracted considerable attention due to their diverse biological activities. By analyzing the genomes of Apium Graveolens L. and Peucedanum praeruptorum Dunn, we characterized a set of candidate genes encoding key enzymes involved in furanocoumarin biosynthesis, including one prenyltransferase (AgPT1), cyclases (AgCOC1, PpCOC1 and PpCOC2), and methyltransferases (AgOMT1 and AgOMT2). Functional validation in Saccharomyces cerevisiae demonstrated that AgCOC1 and PpCOC2 accept both linear and angular substrates, whereas PpCOC1 accepts only linear substrates. Depending on the reaction conditions, these cyclases can produce compounds with either furan or pyran scaffolds. These findings reveal a previously unappreciated catalytic versatility of cyclases involved in furanocoumarin biosynthesis. Notably, the genes encoding the prenyltransferase and cyclases were found to be co-localized in the genome, which may significantly enhance the efficiency of furanocoumarin biosynthesis. This mechanism may account for the pronounced accumulation of furanocoumarins in Apiaceae plants. Finally, we provide the first evidence that AgOMT1 functions as a multifunctional methyltransferase capable of catalyzing the O-methylation modifications observed in furanocoumarins in A. graveolens. In conclusion, this study fills a research gap in our understanding of furanocoumarin biosynthesis and reveals that genes encoding cyclases and prenyltransferases are clustered in the genome, a pattern that arose during evolution.