Schizophyllum commune has an extensive and functional alternative splicing repertoire

Abstract

Recent genome-wide studies have demonstrated that fungi possess the machinery to alternatively splice pre-mRNA. However, there has not been a systematic categorization of the functional impact of alternative splicing in a fungus. We investigate alternative splicing and its functional consequences in the model mushroom forming fungus Schizophyllum commune. Alternative splicing was demonstrated for 2,285 out of 12,988 expressed genes, resulting in 20% additional transcripts. Intron retentions were the most common alternative splicing events, accounting for 33% of all splicing events, and 43% of the events in coding regions. On the other hand, exon skipping events were rare in coding regions (1%) but enriched in UTRs where they accounted for 57% of the events. Specific functional groups, including transcription factors, contained alternatively spliced genes. Alternatively spliced transcripts were regulated differently throughout development in 19% of the 2,285 alternatively spliced genes. Notably, 69% of alternatively spliced genes have predicted alternative functionality by loss or gain of functional domains, or by acquiring alternative subcellular locations. S. commune exhibits more alternative splicing than any other studied fungus. Taken together, alternative splicing increases the complexity of the S. commune proteome considerably and provides it with a rich repertoire of alternative functionality that is exploited dynamically.

Variants in RNA-Seq data show a continued mutation rate during strain preservation ofSchizophyllum commune

“…As S. commune does not need its full functional repertoire in our experiment, we expected some groups to be more mutated than others. For example, strains used in our experiments are always grown on glucose containing minimal medium (Gehrmann et al, 2016), implying that the need for carbohydrate active enzymes (cazymes) is reduced. Yet, we do not observe more mutations in this group of genes due to a lesser evolutionary pressure.…”

“…To characterize the mutation landscape in various steps of an experimental design, we developed a method with which single nucleotide polymorphisms (SNPs) can be identified from the transcriptome (Methods). As the genome of S. commune is very dense, and neighboring genes have overlapping UTRs, the transcriptome spans ~89% of the genome (Gehrmann et al, 2016). This not only permits us to identify mutations that accumulated during culturing of the strain samples across a large portion of the genome but also gives us the ability to study their phenotypic effect across various growth conditions.…”

“…SNPs present in a large number of samples also mapped to genes that have a high RNA expression level (Supplementary Note 7). 9% of the SNPs (1,252) lie in previously predicted alternatively spliced genes (Gehrmann et al, 2016).…”

“…Interpro domain annotations were taken from the JGI DOE website, filtered with a score threshold < 0.05. Transcription factors were predicted based on a curated list of fungal DNA binding domains, as in (Gehrmann et al, 2016). Cytochrome P450 genes were predicted based on the Interpro domain IPR001128, and metabolic genes based on the GO annotation GO:0008152.…”

“…All knockout strains are derived from a wild-type derivative, in which the ku80 gene is deactivated (node 26, Figure 1, Supplementary Note 4) to repress non-homologous chromosomal repair . We studied the accumulation of spontaneous genomic mutations during growth of the wildtype and knockout strains in an experiment to monitor whole genome expression during development of S. commune (Figure 1, Materials) (Gehrmann et al, 2016;.…”