A Global View of Transcriptome Dynamics during Sporisorium scitamineum Challenge in Sugarcane by RNA-seq

Abstract

Sugarcane smut caused by Sporisorium scitamineum is a critical fungal disease in the sugarcane industry. However, molecular mechanistic studies of pathological response of sugarcane to S. scitamineum are scarce and preliminary. Here, transcriptome analysis of sugarcane disease induced by S. scitamineum at 24, 48 and 120 h was conducted, using an S. scitamineum-resistant and -susceptible genotype (Yacheng05-179 and “ROC”22). The reliability of Illumina data was confirmed by real-time quantitative PCR. In total, transcriptome sequencing of eight samples revealed gene annotations of 65,852 unigenes. Correlation analysis of differentially expressed genes indicated that after S. scitamineum infection, most differentially expressed genes and related metabolic pathways in both sugarcane genotypes were common, covering most biological activities. However, expression of resistance-associated genes in Yacheng05-179 (24–48 h) occurred earlier than those in “ROC”22 (48–120 h), and more transcript expressions were observed in the former, suggesting resistance specificity and early timing of these genes in non-affinity sugarcane and S. scitamineum interactions. Obtained unigenes were related to cellular components, molecular functions and biological processes. From these data, functional annotations associated with resistance were obtained, including signal transduction mechanisms, energy production and conversion, inorganic ion transport and metabolism, and defense mechanisms. Pathway enrichment analysis revealed that differentially expressed genes are involved in plant hormone signal transduction, flavonoid biosynthesis, plant-pathogen interaction, cell wall fortification pathway and other resistance-associated metabolic pathways. Disease inoculation experiments and the validation of in vitro antibacterial activity of the chitinase gene ScChi show that this sugarcane chitinase gene identified through RNA-Seq analysis is relevant to plant-pathogen interactions. In conclusion, expression data here represent the most comprehensive dataset available for sugarcane smut induced by S. scitamineum and will serve as a resource for finally unraveling the molecular mechanisms of sugarcane responses to S. scitamineum.

RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease

“…The enrichment analysis of 5-DAI DEGs showed as expected two contrasting molecular responses as previously described [25]. The genes involved in general plant immunity were down-regulated, while those for epigenetic mechanisms were up-regulated (Fig 3).…”

Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem

“…Analysis of the DEGs showed different up and down regulated transcripts in both the interactions. An interaction between sugarcane and Sporisorium scitamineum revealed early expression of defense related genes in the resistant sugarcane genotype in comparison to the susceptible one [42] Although more examples of model as well as non-model plant-fungus interactions have been reported [43, 44, 45, 46, 47], there are only a few reports of differential gene expression between host plants and Colletotrichum species using RNA-seq. In total, these studies have led to a better understanding of the early defense signaling mechanisms during pathogen infection and proliferation.…”

Defense-related proteins involved in sugarcane responses to biotic stress

“…coeruleum (Que et al , 2014). Moreover, sugarcane chitinases showed action against C. falcatum and are also associated with Pseudomonas -mediated induced resistance (Viswanathan et al , 2003) and with sugarcane response to D. saccharalis attack (Medeiros et al ., 2012).…”