Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen

Author(s)

Bedre, Renesh ^[1] ; Irigoyen, Sonia ^[1] ; Schaker, Patricia D. C. ^{[2, 3]} ; Monteiro-Vitorello, Claudia B. ^[2] ; Da Silva, Jorge A. ^{[4, 1]} ; Mandadi, Kranthi K. ^{[1, 5]}

Affiliation

^[1] Texas A&M Univ, Texas A&M AgriLife Res & Extens Ctr, Weslaco, TX 78599 - USA

^[2] Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Genet, Piracicaba, SP - Brazil

^[3] Univ Tecnol Fed Parana, Toledo, Parana - Brazil

^[4] Texas A&M Univ, Dept Soil & Crop Sci, College Stn, TX 77843 - USA

^[5] Texas A&M Univ, Dept Plant Pathol & Microbiol, College Stn, TX 77843 - USA

• Document type: Journal article
• Source: SCIENTIFIC REPORTS; v. 9, JUN 20 2019.
• Web of Science Citations: 1

Abstract

Alternative splicing (AS) promotes transcriptome and proteome diversity during growth, development, and stress responses in eukaryotes. Genome-wide studies of AS in sugarcane (Saccharum spp.) are lacking, mainly due to the absence of a high-quality sequenced reference genome, sugarcane's large, complex genome, and the variable chromosome numbers and polyploidy of sugarcane cultivars. Here, we analyzed changes in the sugarcane isoform-level transcriptome and AS landscape during infection with the smut fungus (Sporisorium scitamineum) using a hybrid approach involving Sorghum bicolor reference-based and Trinity de novo mapping tools. In total, this analysis detected 16,039 and 15,379 transcripts (>= 2 FPKM) at 5 and 200 days after infection, respectively. A conservative estimate of isoform-level expression suggested that approximately 5,000 (14%) sugarcane genes undergo AS. Differential expression analysis of the alternatively spliced genes in healthy and smut-infected sugarcane revealed 896 AS events modulated at different stages of infection. Gene family and gene ontology functional enrichment analysis of the differentially spliced genes revealed overrepresentation of functional categories related to the cell wall, defense, and redox homeostasis pathways. Our study provides novel insight into the AS landscape of sugarcane during smut disease interactions. (AU)

• FAPESP's process: 17/02434-9 - Identification of receptor proteins of effectors from the sugarcane smut pathogen Sporisorium scitamineum
• Grantee: Patricia Dayane Carvalho Schaker
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 17/13268-2 - Genomic and functional studies of the interaction Sporisorium scitamineum-cana and other smut fungi: advances and challenges
• Grantee: Claudia Barros Monteiro Vitorello
• Support Opportunities: Regular Research Grants