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.
Highlights
Sugarcane (Saccharum spp., Poaceae family) is a high-value C4 grass with a global estimated harvest yield of ~1.89 billion tons in 20161, contributing to ~75% of sugar and ~60% of ethanol production worldwide[2,3]
Splicing by the spliceosome complex composed of small nuclear riboproteins occurs at exon-intron splice sites, usually GT-AG, which play a major role in forming alternative transcripts[22]
We used a hybrid transcriptome mapping approach to determine alternative splicing (AS) patterns and alternatively spliced genes in sugarcane in response to infection with a biotrophic smut fungus
Summary
Sugarcane (Saccharum spp., Poaceae family) is a high-value C4 grass with a global estimated harvest yield of ~1.89 billion tons in 20161, contributing to ~75% of sugar and ~60% of ethanol production worldwide[2,3]. Considering annual increases in prevalence of sugarcane smut disease and lack of control strategies, development of smut-resistant sugarcane varieties has emerged as a key priority. Integrative proteomics and transcriptomics analysis identified 273 and 341 differentially expressed proteins in smut-resistant and susceptible sugarcane genotypes, respectively[13]. These studies reveal significant information about the various transcription-level changes occurring during sugarcane–smut interactions. The extent of genome-wide changes in a key post-transcriptional process, alternative splicing (AS), in sugarcane has not yet been reported This is mainly due to the lack of a sequenced reference genome and the daunting genome-level complexity of sugarcane hybrids with large polyploid genomes (~10 Gbp) and varying numbers of chromosomes[15,16,17]. AS is modulated during plant growth and development, photosynthesis, metabolic pathways, circadian clock function, and flowering[22,26]
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