Genome-Wide Identification and Analysis of Alternative Splicing in <i>Aspergillus niger</i>

Aspergillus niger  is a widely used fungal species in fermentation industry. Identifying genes having RNA transcripts undergoing alternative splicing (AS) is important for understanding the gene expression regulations and finding novel enzymes for bioprocessing applications. In this study, we combined genome mapping information of all available RNA sequences and expressed sequence tags in the public database with RNA-seq data collected from 303 publicly available samples for identification of AS events in A. niger . We identified a total of 63,715 AS events including 10,097 (15.8%) alternative acceptor sites (AltA), 6,063 (9.5%) alternative donor sites (AltD), 12,469 (19.6%) intron retention sites (IntronR), 1,945 (3.1%) exon skipping sites (ExonS), and 33,141 (52.0%) complex events which contained two or more basic events in pairs of compared isoform transcripts. These AS events were identified from 4,972 genes involving 43,156 unique transcripts. The AS rate among all expressed genes was estimated to be ~50.0% in A. niger . Protein coding genes having protein family matches were estimated having 68.0% AS rate, including 52 of 84 genes coding for carbohydrate degrading enzymes (CAZymes) alternatively spliced. The functions of these proteins encoded by alternatively splicing generated isoforms need to be further investigated. We also identified a total of 1,592 new genomic loci with 3,388 transcripts that were not annotated in the reference genome. The AS data and genomic mapping data collected in this study provide a resource for further exploration of novel genes and enzymes in A. niger .