Algae are a large group of organisms that are of ecological and economical importance, as they play an important role in the food web and the biogeochemical cycle, and some of them are found to be suitable for biofuel production. Under stress conditions, they accumulate a large amount of storage lipid. However, the mechanistic details of this phenomenon are not yet well understood. Towards deciphering this phenomenon, I focused on characterizing gene expression changes and gene family evolution in the context of stress response in two micro-algal species. I first analyzed the global gene expression changes of the green alga model organism Chlamydomonas reinhardtii under normal and nitrogen deprived conditions. I found that global gene expression changes significantly under nitrogen deprivation; lipid metabolism was associated with up-regulated genes while DNA replication and photosynthesis were down-regulated. Second, I outlined global gene family evolution in the green algal lineage, particularly in the extent of duplicate retention and loss, and stress response evolution among duplicates. I found that stress responsive genes tend to be lineage-specifically retained and functional gains occur frequently in gene duplicates, shaping the stress response gene repertoire in a species-specific manner. Finally, I assembled and annotated the genome of the stramenopile Nannochloropsis oceanica CCMP1779, a phylogenetically distant species to C. reinhardtii considered for biofuel production. I found that N. oceanica responds similarly to nitrogen deprivation as C. reinhardtii, suggesting that general metabolic change is conserved across distantly related species. In addition, we compared the N. oceanica genome to Nannochloropsis gaditana to reveal its uniqueness in gene repertoire. We found that it is significantly different from N. gaditana and this might reflect physiological and biochemical differences. Overall, I reveal that though major metabolic changes under stress in micro-algae across diverse phylogeny are similar, the particular genes involved in stress response could be significantly different as they have been shaped by lineage-specific evolution. Thus, the species-specific mechanism in stress response cannot be deciphered by studying one model organism. Therefore, it would be beneficial to explore more micro-algal species, especially the ones considered for biofuel production, to discover their uniqueness in stress response towards identifying and engineering the ideal alga for biofuel production.
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