A global view of transcriptome dynamics during Sporisorium scitamineum challenge in sugarcane by RNA-Seq

PLoS One. 2014 Aug 29;9(8):e106476. doi: 10.1371/journal.pone.0106476. eCollection 2014.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Disease Resistance
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Plant
  • Plant Diseases / microbiology
  • Plant Proteins / genetics*
  • RNA, Plant / analysis
  • Saccharum / classification
  • Saccharum / genetics*
  • Saccharum / microbiology
  • Ustilago / pathogenicity*

Substances

  • Plant Proteins
  • RNA, Plant

Grants and funding

This work was funded by National Natural Science Foundation of China (31101196 and 31340060), the earmarked fund for the Modern Agriculture Technology of China (CARS-20), Program for New Century Excellent Talents in Fujian Province University (2014) and Research Funds for Distinguished Young Scientists in Fujian Agriculture and Forestry University (xjq201202). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.