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

Abstract

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.

Evolutionary divergence of photoprotection in the green algal lineage: a plant‐like violaxanthin de‐epoxidase enzyme activates the xanthophyll cycle in the green alga Chlorella vulgaris modulating photoprotection

“…Moreover, an exponential correlation between the induction of NPQ and zeaxanthin accumulation was found, suggesting that additional components are contributing to NPQ induction, especially at higher actinic light intensities. These could be LHC-like proteins involved in quenching, such as PSBS and light-harvesting complex stress-related (LHCSR), recently reported also in the case of C. vulgaris (Cecchin et al, 2019). Alternatively, other LHCII proteins that present protonatable sites (Walters et al, 1996;Li et al, 2004;Liguori et al, 2013;Ballottari et al, 2016) could be responsible for the modulation of the extent of NPQ at different actinic light intensities, independently from the contribution of zeaxanthin.…”

The desert green algaeChlorella ohadiithrives at excessively high light intensities by exceptionally enhancing the mechanisms that protect photosynthesis from photoinhibition

“…This may have been the result of their evolutionary elimination since in the absence of the trimeric LHCII, the LHCSR does not protect from PI. Notably, the LHCSR genes are present in another Chlorella species, C. vulgaris (Cecchin et al, 2019). However and as noted above, two psbS genes are present and their transcripts are elevated in high light treated cells (Treves et al, 2020).…”

Molecular and Structural Characterizations of Lipases from Chlorella by Functional Genomics

“…Recently, its whole genome sequence was revealed by next-generation sequencing technologies, and the major metabolic pathways were identified [ 13 ]. Lipid metabolism has also been analyzed in multi-omics studies, including transcriptomics and proteomics to obtain the mechanistic insight of its lipid biosynthesis [ 14 ]. However, the TAG lipases have not been investigated yet.…”