Computational Molecular Biology 2025, Vol.15, No.1, 1-12 http://bioscipublisher.com/index.php/cmb 10 4 Discussion We integrated mapping information of more than 10 billion of RNA-seq reads generated from 303 samples collected from eight recently published articles with 19,571 assembled transcripts of mRNA mapping information for identification of genome-wide AS events in A. niger. To our knowledge, this is the first large scale genome-wide meta-analysis of AS events in A. niger using RNA-seq data collected from various growth substrates. Combining all the mapping data generated a total of 9,939 genomic loci with a total of 66,007 transcripts assembled. A total of 63,715 AS events were identified from 4,972 genomic loc involving 43,156 unique transcripts. The AS rate based on current work was estimated to be about 50.0% in A. niger. We expect that more AS events and a higher AS rate can be obtained when more RNA-seq or transcripts data are integrated for genome mapping in A. niger in future. The impact of AS events on the encoded protein functions including enzymes needs to be evaluated individually. Our data including the assembled transcript sequences and mapping files are publicly available for the community to experimentally verify the identified isoform sequences and explore their functional novelties of enzymes for bioprocessing applications. The work represents a large scale of genome-wide systematic identification of alternatively spliced genes and isoforms in A. niger. As in our analysis showed AS in genes in fungal species may be a common process, we recommend that researchers working in fungal species consider AS analysis when performing transcriptomic studies. However, it should be noted that these isoform transcript sequences were assembled by Cufflinks, validation by RT-PCR or cloning the full-length of mRNA transcripts are needed for further detailed functional analysis. The work carried out by Xu et al. (2024) in lignocellulos-degrading enzyme genes and enzyme variants in A. niger can serve as an example for this type of analysis. Computational identification of genes undergoing AS and annotation of their associated transcript isoform sequences are useful for researchers to design more specific experiments to examine the functions of genes of interests. The current work provides an important resource for investigating alternatively spliced genes and their associated functions of protein isoforms in A. niger. The data are expected to be useful in identifying homologous alternatively spliced genes in other fungal species in future research. Author Contributions XM designed the experiments. XM and FY provided the methodology, software support, and data analysis. XM, CJ, BL, MC, BW, CD, AP, PM, and KA carried out RNA-seq and mRNA transcript data collection and genome mapping. XM and FY prepared the manuscript. All authors have read and agreed to the published version of the manuscript. Acknowledgements The Ohio Supercomputer Center provided computational resources for part of data processing. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Boel E., Hjort I., Svensson B., Norris F., Norris K.E., Fiil N.P., 1984, Glucoamylases G1 and G2 fromAspergillus niger are synthesized from two different but closely related mRNAs, EMBO J., 3(5): 1097-1102. https://doi.org/10.1002/j.1460-2075.1984.tb01935.x Borin G.P., Sanchez C.C., de Souza A.P., de Santana E.S., de Souza A.T., Leme A.F., Squina F.M., Buckeridge M., Goldman G.H., Oliveira J.V., 2015, Comparative secretome analysis of Trichoderma reesei and Aspergillus niger during growth on sugarcane biomass, PLoS One, 10(6): e0129275. https://doi.org/10.1371/journal.pone.0129275 Cairns T.C., Nai C., Meyer V., 2018, How a fungus shapes biotechnology: 100 years of Aspergillus niger research, Fungal Biol. Biotechnol., 5: 1-4. https://doi.org/10.1186/s40694-018-0054-5 Chaudhary S., Khokhar W., Jabre I., Reddy A.S., Byrne L.J., Wilson C.M., and Syed N.H., 2019, Alternative splicing and protein diversity: plants versus animals, Front. Plant Sci., 10: 708. https://doi.org/10.3389/fpls.2019.00708 Clark S., Yu F., Gu L., and Min X.J., 2019, Expanding alternative splicing identification by integrating multiple sources of transcription data in tomato, Front. Plant Sci., 10: 689. https://doi.org/10.3389/fpls.2019.00689
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