Integrative analysis of gene expression and alternative splicing in microalgae grown under heterotrophic condition

Heterotrophic cultures are the most effective approach to overcome low growth rate challenge in the most commercial microalgae. However, the mechanism through which heterotrophic condition regulates algae metabolism are not completely clear. Alternative Splicing (AS) is a common posttranscriptional process by which transcriptome and proteome plasticity increases at different environmental conditions. To identify and characterize of AS events in Auxenochlorella protothecoides microalga grown in autotrophic and heterotrophic, RNA-Seq data were analysed. We found that AS increased with the transition from autotrophic to heterotrophic condition. 705 and 660 differentially expressed (DEG) and spliced (DAS) genes were identified for A.protothecoides was transferred from autotrophic to heterotrophic condition, respectively. Moreover, there was slight coverage between DEG and DAS genes. Furthermore, functional analysis showed that the DAS genes are most frequently related to ion binding and stimulus response. The results also indicated that prevalence of Intron retention is associated with down-regulation of the genes involved in carotenoid biosynthesis. This study provides valuable insights into transcriptional and posttranscriptional plasticity of microalgae during growth mode change.