Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions.
Michela CecchinLuca MarcolungoMarzia RossatoLaura GirolomoniEmanuela CosentinoStephan CuineYonghua Li-BeissonMassimo DelledonneMatteo BallottariPublished in: The Plant journal : for cell and molecular biology (2019)
Chlorella vulgaris is a fast-growing fresh-water microalga cultivated on the industrial scale for applications ranging from food to biofuel production. To advance our understanding of its biology and to establish genetics tools for biotechnological manipulation, we sequenced the nuclear and organelle genomes of Chlorella vulgaris 211/11P by combining next generation sequencing and optical mapping of isolated DNA molecules. This hybrid approach allowed us 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-seq data obtained at two different irradiances of growth (high light, HL versus low light, LL) enabled us to identify 10 724 nuclear genes, coding for 11 082 transcripts. Moreover, 121 and 48 genes, respectively, were found in the chloroplast and mitochondrial genome. Functional annotation and expression analysis of nuclear, chloroplast and mitochondrial genome sequences revealed particular features of Chlorella vulgaris. Evidence of horizontal gene transfers from chloroplast to mitochondrial genome was observed. Furthermore, comparative transcriptomic analyses of LL versus HL provided insights into the molecular basis for metabolic rearrangement under HL versus LL conditions leading to enhanced de novo fatty acid biosynthesis and triacylglycerol accumulation. The occurrence of a cytosolic fatty acid biosynthetic pathway could be predicted and its upregulation upon HL exposure was observed, consistent with the increased lipid amount under HL conditions. These data provide a rich genetic resource for future genome editing studies, and potential targets for biotechnological manipulation of Chlorella vulgaris or other microalgae species to improve biomass and lipid productivity.
Keyphrases
- genome wide
- rna seq
- fatty acid
- single cell
- genome editing
- dna methylation
- copy number
- crispr cas
- oxidative stress
- poor prognosis
- high resolution
- electronic health record
- wastewater treatment
- risk assessment
- arabidopsis thaliana
- human health
- climate change
- big data
- long non coding rna
- signaling pathway
- machine learning
- mass spectrometry
- transcription factor
- high speed
- case control