The effects of mutations on gene expression and alternative splicing: a case study of EMS-induced heritable mutations in the microcrustacean Daphnia

Understanding the relationship between mutations and their genomic and phenotypic consequences has been a longstanding goal of evolutionary biology. However, few studies have investigated the impact of mutations on gene expression and alternative splicing on the genome- wide scale. In this study, we aim to bridge this knowledge gap by utilizing whole-genome sequencing data and RNA sequencing data from 16 OP Daphnia mutant lines to investigate the effects of EMS-induced mutations on gene expression and alternative splicing. Using rigorous analyses of mutations, expression changes, and alternative splicing, we show that trans-effects are the major contributor to the variance in gene expression and alternative splicing between the wildtype and mutant lines, whereas cis mutations only affected a limited number of genes and do not always alter gene expression. Moreover, we show that there is a significant association between DE genes and exonic mutations, indicating that exonic mutations are an important driver of altered gene expression.