Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions

Chlorella vulgaris is a fast-growing fresh-water microalga cultivated at the industrial scalefor applicationsrangingfrom food to biofuel production. To advance our understanding of its biology andto establishgenetics toolsfor biotechnological manipulation, we sequenced the nuclear and organelle genomes of Chlorella vulgaris211/11Pbycombining next generation sequencing and optical mappingof isolated DNA molecules. This hybrid approach allowed to assemble the nuclear genome in 14 pseudo-molecules with an N50 of 2.8 Mb and 98.9% of scaffolded genome. The integration of RNA-seqdata obtained at two different irradiances of growth(high light-HL versus low light -LL)enabled to identify 10,724 nuclear genes, coding for 11,082 transcripts. Moreover 121 and 48 genes were respectively found in the chloroplast and mitochondrial genome.Functionalannotationand expression analysis of nuclear, chloroplast and mitochondrial genome sequencesrevealed peculiarfeatures of Chlorella vulgaris. Evidence of horizontal gene transfersfrom chloroplast to mitochondrial genome was observed. Furthermore, comparative transcriptomic analyses of LL vs HL provide insights intothe molecular basis for metabolic rearrangement in HLvs. LLconditions leading toenhancedde novofatty acid biosynthesis and triacylglycerol accumulation.The occurrence of a cytosolic fatty acid biosynthetic pathway can be predicted and its upregulation upon HL exposure is observed, consistent with increased lipid amount under HL. These data provide a rich genetic resource for future genome editing studies, andpotential targets forbiotechnologicalmanipulationof Chlorellavulgarisor other microalgae speciesto improve biomass and lipid productivity