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Ratoon stunt caused by Leifsonia xyli subsp. xyli (Lxx) is widely spread across sugarcane planting regions. Here, transcriptomics and cytology were conducted to analyze the changes in gene expression levels and chloroplast ultrastructures after Lxx inoculation. A total of 90.26 Gb clean bases, 156,713 unigenes and 406 differentially expressed genes were obtained. The genes of HSP and ACS were continuously differentially expressed. The photosynthesis-related genes of PsbO, PsbQ, PsaD, PsaE, PsaG and PsaH were up-regulated. PIRH2, WRKY, NCED, AHP and GST were identified as the important specific genes that responded to Lxx inoculation. Lxx inoculation also altered the shape and damaged the membrane of chloroplasts in sugarcane leaves. Sugarcane responds to Lxx infection likely via changing the expression levels of some specific genes and interfered with photosynthesis. A possible molecular regulation network induced by Lxx was speculated. These findings broaden the understanding to the mechanisms of the interaction between sugarcane and Lxx.

Fusarium verticillioides is the pathogen associated with pokkah boeng disease (PBD), the most significant airborne disease of sugarcane. The molecular mechanisms that regulate the defense responses of sugarcane towards this fungus are not yet fully known. Samples of 'YT 94/128' (resistant, R) and 'GT 37' (susceptible, S) inoculated with F. verticillioides on the 14 days post-inoculation were used to analyze the transcriptome to screen R genes. In total, 80.93 Gb of data and 76,175 Unigenes were obtained after assembling the sequencing data, and comparisons of Unigenes with NR, Swiss-prot, KOG, and KEGG databases confirmed 42,451 Unigenes. The analysis of differentially expression genes (DEGs) in each sample revealed 9092 DEGs in 'YT 94/128,' including 8131 up-regulated DEGs and 961 down-regulated DEGs; there were 9829 DEGs in 'GT 37,' including 7552 up-regulated DEGs and 2277 down-regulated DEGs. The identified DEGs were mainly involved in catalytic enzyme activity, cell protease, hydrolytic enzymes, peptide enzyme, protein metabolism process of negative regulation, phenylpropanoid metabolism, extracellular region, aldehyde dehydrogenase, endopeptidase, REDOX enzyme, protein kinases, and phosphoric acid transferase categories. KEGG pathway clustering analysis showed that the DEGs involved in resistance were significantly related to metabolic pathways of phenylpropanoid biosynthesis, cutin, suberine and wax biosynthesis, nitrogenous metabolism, biosynthesis of secondary metabolites, and plant-pathogen interactions. This application of transcriptomic data clarifies the mechanism of interactions between sugarcane and F. verticillioides, which can help to reveal disease-related metabolic pathways, molecular regulatory networks, and key genes involved in sugarcane responses to F. verticillioides.

Background Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied. Results Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane. Conclusions The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.