- Results: In the present study, we first obtained high-quality long transcripts from the internodes of sugarcane using the PacBio Sequel System. - Furthermore, the qPCR validated the high accuracy of the RNA-seq results.. - To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. - About 80% of the world’s sugar is isolated from sugarcane, making it a critical bioenergy crop [26]. - Moreover, to venture into this knowledge would require thorough scanning of the systematic regu- lation of DPC in plants.. - At the beginning of the experi- ment (0 days), no significant difference was found be- tween the control and DPC groups (P>. - However, the sugarcane heights on days 3, 6, and 12 as well as that of mature sugarcane, were significantly higher in the control than in the DPC groups (P<. - More- over, all the internodes were significantly longer in the control group (Fig. - In the biological process category, metabolic process (13,462 isoforms) and cellular process (12,836 isoforms) were the two most functional terms. - The first principal component, PC1, summarized 30.7% of the whole variability and discriminated samples according to the treatment. - The second principal component, PC2, and the third principal component, PC3, summarized 25.1 and 17.4% of the whole variability and discrimi- nated samples, respectively. - Functional analyses of DEGs between C2 and D2 groups To illustrate the functions of the DEGs after DPC treat- ment, GO enrichment and KEGG enrichment analyses of the comparison of C2 and D2 with the most DEGs were performed. - KEGG enrichment analysis showed that 17 and 30 pathways were enriched in the upregulated and downregulated genes, respectively (Fig. - Meanwhile, phenylpropanoid biosynthesis, flavonoid biosynthesis, favone and flavonol biosynthesis, and glucosinolate biosynthesis were enriched in the downregulated genes (Additional file 5). - Except for GID2 and PBS1, the other six tested genes, GA2OX1, GID1, MPK4, CML49, PRPF8, and ACO2, showed simi- lar qPCR results to those of the RNA-seq. - These results showed the high reliability of the RNA-Seq data.. - Sugarcane is the main source of sugar in the industry, accounting for 79% of the sugar production worldwide.. - Thus, in the present study, we focused on the transcriptomic regulation by DPC on sugarcane and discussed the key genes that mediate its growth- suppressive effect.. - Notably, it turns out that the N50 was 3073 for the isoforms in the present study. - DPC is one of the most successful and widely used chemicals for regulating plant growth. - After understand- ing the effects of DPC on internode growth, the next question is to determine the molecular mechanism of the function of DPC in sugarcane. - The KEGG enrichment analysis showed that the ex- pression levels of 55 genes in the plant hormone signal transduction pathway had increased from DPC treat- ment. - Therefore, the most critical genes play a key role in the module. - These three hub genes were correlated with the other genes in the si- enna3 modules. - Additionally, the gene modules included 33 genes that were highly correlated with the stage of six days post spraying in the DPC group, showing a potential role in the response to DPC.. - d GO annotation of the isoforms. - a Principle component analyses of the 18 transcriptomes from the internodes of sugarcane on different days, in the control and DPC treatment groups, based on the FPKM. - Similarly, the samples of the DPC group from 3, 6, and 12 days post spraying were named D1, D2, and D3, re- spectively. - Sugarcane growth performance was measured in the control and DPC groups. - At 3, 6, and 12 days post spraying, we measured the stalk height from the soil surface to the dewlap of the youngest fully expanded leaf, as well as the length of the internodes. - The quantity and integrity of the total RNA was assayed using an Agilent 2100 bioanaly- zer (Agilent, Santa Clara, CA, USA). - c Cluster dendrogram of the dissimilarity clustering using a consensus topological overlap.. - 7 Heatmap of the module-trait relationship between different groups and gene modules. - www.r-project.org/) to evaluate the reproducibility of the biological replicates. - Further, the FPKM matrix of the retained genes was used to create a weighted adja- cency matrix. - of the D2 group for further analysis. - The line charts show the log 2 (FPKM) values of the genes, and the bar charts show the relative expression from qPCR results. - The top three hub genes were identified using Cytohubba (http://apps.cytoscape.org/apps/cytohubba) and the network was plotted using Cytoscape v3.7.1.. - Real-time quantitative PCR analysis of genes (qPCR) Total RNA from internode tissues in the control and DPC groups were isolated and tested as described in sec- tion 2.1. - To confirm the specificity of the PCR reaction, a melt curve analysis was performed. - Additionally, the relative expression of the genes was calculated by the 2 - 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