Computational Molecular Biology 2025, Vol.15, No.1, 1-12 http://bioscipublisher.com/index.php/cmb 6 knife-milled wheat straw (KMS) (Daly et al. 2017; van Munster et al. 2020). We combined all samples collected over a 5-day time course for each treatment for identification AS events, the results were summarized (Table 7). The differences in total numbers of AS events were mostly caused by the data size differences in these treatments (R2 = 0.9603) (Figure 1). The similar trend of positive relationship between numbers of AS events and mapped RNA-seq reads was reported in our previous analysis with data collected from potato plants (Lee and Min 2023). To detect the effects of different treatments on AS events, we carried out pairwise comparisons of AS events in these treatments of combined data (Figure 2-4). Clearly, AS events were dynamically changed with different treatment of growth substrates in glucose, differently pretreated Miscanthus, and differently pretreated wheat straws. There were conserved AS events among all treatments as well as treatments specifically generated AS events (Figure 2-4). Daly et al. (2017) and van Munster et al. (2020) reported dynamic transcriptomic expressions of CAZymes at gene levels in different pretreated growth substrates over a time course. Our analysis demonstrated AS events were also dynamically regulated in these treatments. More detailed analysis would allow to identify treatment specific AS events and novel isoforms for further exploration of novel enzymatic activities for applications in the biofuel production. Figure 1 Relationships of total mapped reads and total alternative splicing events identified in seven different treatments of growth substrates inA. niger Figure 2 Alternative splicing events identified in glucose (GLU), hydrothermal pretreated Miscanthus (HTM), ionic liquid pretreated Miscanthus (ILM), and knife-milledMiscanthus (KMM) as substrates for A. niger culture
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