System-Wide Transcriptome Analysis Delineate Lipid Regulatory Pathways in Microalgae

In the effort to explore alternative renewable energy, biofuel represents a major promise towards to an efficient and effective solution. Among different sources, microalgae biodiesel offers great potential to provide highest production efficiency and oil-rich algae have proven to be an outstanding model for their ability to produce lipids as the most effective precursors. Thus, transcriptional regulation on the genetic pathways maximizing the production of lipids and their precursor TAG has been the center of algae biodiesel research, yet the comprehensive transcriptome profiling and the systematic interrogation on lipid biosynthetic pathways are still lacking. Chlamydomonas reinhardtii is an unicellular green algae whose simple life cycle and ease of genetic manipulation have made it a popular organism for biodiesel study. Here, we performed an unprecedented survey on transcriptomic analysis of fine resolution supported by Kapa stranded RNA-seq technology through Illumina SBS sequencing and PacBio Iso-seq in this major model alga to decipher the regulation network of lipid biosynthesis. From over 500 million sequences, we found more than half of the genome was transcribed into over 22,000 expressed coding transcripts and thousands of putative small RNAs with microRNA characteristics. Furthermore, we are able to identify the dynamic transcriptional components of the regulatory pathways responsible for TAG biogenesis and accumulation with high temporal resolution. The differentially expressed genes including transcriptional factors, non-coding RNA and coding splice variants allow us to reconstruct the biodiesel pathways that can be confirmed by histone modification occupancy. Our results suggest the complex interplay between multiple cellular RNA components in unicellular green algae and provide a robust framework to enable system-wide genetic manipulation in algae biodiesel regulation