Depicting Dual Transcriptome Profiles of Early and Late Responses of Sugarcane Interaction with the Biotrophic Fungus Sporisorium scitamineum, the Causal Agent of Smut Disease

Sugarcane smut disease is caused by the biothrophic  fungus Sporisorium scitamineum. The main symptoms of the disease are the emission of a whip-like structure composed by fungi and plant cells, reduced growth, increased fiber and lowered sucrose contents. RNAseq gene expression profiles were depicted to shed light on the sugarcane responses  during development of the disease. Early responses were analyzed five days after infection of mechanically injured buds covered with a paste of teliospores and compared to non inoculated buds of cultivar RB92-5345. Late responses were analyzed immediately after the whip emission. The base of the whip (4 cm below whip emission)  where fungal sporogenesis takes place were collected and compared with control plants of the same age (200 days). All treatments were performed with 3 replicates. Total RNA were prepared using lithium chloride based extraction. For the construction of pair-end RNA-seq libraries, all procedures were according to Illumina manufacturer’s instructions using the ‘TruSeq RNA Sample Prep v2 Low Throughput (LT)’ kit. RNAseq data analysis were mostly conducted on the CLC Genomics Workbench Platform V5 comparing each treatment with their respective controls. MapMan V3.5 analysis and visualization tool organized the data within specific metabolic pathways.   Reference genomes used were the annotated version of Sorghum bicolor coding sequences (V1.4 Phytozome) and a draft genome sequence of a Brazilian isolated of  S. scitamineum.  RNAseq data of early interaction resulted in close to 112 million reads, of that only about 2% mapped Sporisorium genome. Late interaction resulted in 113 million reads and close to 20% of the reads mapped the fungus genome. Total sugarcane transcripts mapped  25,843 sorghum genes out of the 29,448 predicted as protein-encoding. A total of 106 sugarcane predicted- sorghum based- genes were defined as differentially expressed in early stage of the interaction process compared to control using a combination of bioinformatics tools besides CLC (FDR value of 10%). Among them are genes related to stress responses to fungi and other pathogens, general oxidative stress responses and auxin responsive proteins . For late interaction, 555 genes where differentially expressed compared to the control plants of the same age (CLC; FDR 5%).  Highlights of sugarcane differential gene expression profiles in this second moment of infection are the modulation of genes related to hormones and carbohydrate metabolism (plant cell wall and sucrose). By exploring sugarcane transcriptome at different stages of infection, we hope to contribute to a better understanding of the smut disease establishment in sugarcane.