Systematic Genome-wide Identification and Analysis of Alternative Splicing in the Pathogenic Fungus Talaromyces marneffei

Talaromyces marneffei , a thermally dimorphic saprophytic fungus, causes talaromycosis in immunocompromised patients. Differential gene expressions determine the morphology of this species at different growing temperatures. It is known that alternative splicing (AS) is common in eukaryotes, including fungal species, however, there is not a systematic AS analysis yet in T. marneffei . We collected over 2.3 billion paired RNA-sequencing reads and mapped these reads to the reference genome. A total of 36,769 AS events, including 3,512 alternative acceptor sites, 2,216 alternative donor site, 219 exon skipping, 12,442 intron retention, and 18,380 other events were identified by the genome-wide mapping analysis. These AS events were identified from 1,734 protein-coding gene models and 752 newly identified genomic loci, including 46 genes encoding carbohydrate active enzymes. The AS rate was estimated to be ~19.8%. A total of 46,249 unique RNA transcripts were assembled and 45,296 polypeptides were predicted and functionally annotated. Preliminary analysis using data collected from samples grown at 25°C and 37°C or in dimorphic transitions by switching temperatures identified treatment specific events, suggesting that AS may play some roles in establishing specific morphological characteristics in this species. The data collected in the work, including RNA-seq data mapping information, assembled RNA transcripts, identified AS events, and new genomic loci, provide a solid resource for further investigation of the gene regulations in the dimorphism of T. marneffei .