ArticleScientific reports2019
Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 31 citations in OpenAlex.
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.Bioinformatics advances · 2026Article
- Chromosome-level comparative genomics and host-specific fungal transcriptomics uncover adaptive virulence strategies in the sugarcane smut pathogen.BMC genomics · 2025Article
- LncRNAs co-expressed with targeted genes to regulate sugarcane response to Sporisorium scitamineum infection.Plant cell reports · 2025Article
- Polyploidization: A Biological Force That Enhances Stress Resistance.International journal of molecular sciences · 2024Review
- The subgenome Saccharum spontaneum contributes to sugar accumulation in sugarcane as revealed by full-length transcriptomic analysis.Journal of advanced research · 2023Article
- Cell-type-specific alternative splicing in the Arabidopsis germline.Plant physiology · 2023Article
- WGCNA Identifies a Comprehensive and Dynamic Gene Co-Expression Network That Associates with Smut Resistance in Sugarcane.International journal of molecular sciences · 2022Article
- Alternative Splicing and Its Roles in Plant Metabolism.International journal of molecular sciences · 2022Review
- Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane (Frontiers in plant science · 2022Article
- Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions toFrontiers in plant science · 2022Article
- Comprehensive identification and analysis of circRNAs during hickory (Frontiers in plant science · 2022Article
- The THO/TREX Complex Active in Alternative Splicing Mediates Plant Responses to Salicylic Acid and Jasmonic Acid.International journal of molecular sciences · 2021Article
- HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis.Scientific reports · 2021Article
- The Resistance of Narrow-Leafed Lupin toInternational journal of molecular sciences · 2021Article
- The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns.Frontiers in plant science · 2021Article
- GenFam: A web application and database for gene family-based classification and functional enrichment analysis.Plant direct · 2019Article
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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