Genome-wide Analysis of Alternative Splicing in Aspergillus fumigatus in Response to Different Carbon Sources

Aspergillus fumigatus is a saprophytic filamentous fungus that has evolved into an opportunistic pathogen, particularly affecting immunocompromised individuals. RNA sequencing (RNA-seq) experiments have been conducted to investigate the differential gene expression in wild type and cotA mutant of A. fumigatus in response to different carbon sources. We used the RNA-seq data generated by Martin-Vincete et al. (2024) to investigate alternative splicing (AS) landscape in A. fumigatus growing in different carbon sources including glucose, acetate, and ethanol. Comparison of AS profiles between the wild-type strain and cotA mutant in each carbon source identified strain specific and carbon source specific AS events. Combining all RNA-seq mapping data we identified a total of 341 exon skipping (ES), 1,404 alternative donor site (AltD), 3,024 alternative acceptor site (AltA), 10,312 intron retention (IR), and 12,898 other splicing events. Among 9,857 reference gene models, 2,823 gene models with pre-RNA transcripts were alternatively spliced, including 86 carbohydrate active enzymes, thus the AS rate was estimated to be about 28.6% in A. fumigatus . A total of 53,270 RNA transcripts were assembled, based on RNA-seq mapping information, and were functionally annotated. Strain and carbon source specific differentially expressed transcripts were identified. The collected data including RNA-seq mapping information, assembled transcripts, and identified AS events provide a foundation for further investigation of the gene regulations in A. fumigatus .