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. 2020 Feb 6;9(6):e00896-19. doi: 10.1128/MRA.00896-19

Draft Genome Sequence of the Biofuel-Relevant Microalga Desmodesmus armatus

Eric P Knoshaug a,✉, Ambarish Nag b, David P Astling c, Damien Douchi a, Lieve M L Laurens a
Editor: Jason E Stajichd
PMCID: PMC7005114  PMID: 32029566

A draft genome of 906 scaffolds of 115.8 Mb was assembled for Desmodesmus armatus, a diploid, lipid- and storage carbohydrate-accumulating microalga proven relevant for large-scale, outdoor cultivation, and serves as a model alga platform for improving photosynthetic efficiency and carbon assimilation for next-generation bioenergy production.

ABSTRACT

A draft genome of 906 scaffolds of 115.8 Mb was assembled for Desmodesmus armatus, a diploid, lipid- and storage carbohydrate-accumulating microalga proven relevant for large-scale, outdoor cultivation, and serves as a model alga platform for improving photosynthetic efficiency and carbon assimilation for next-generation bioenergy production.

ANNOUNCEMENT

Microalgae, having higher annual biomass production relative to terrestrial crops and potential for cultivation in salt water on nonarable lands, are critical future feedstocks for renewable liquid fuels (1–4). Desmodesmus, taxonomically divergent from the genus Scenedesmus (5, 6), has been shown to exhibit phenotypic plasticity and resilience, allowing survival in harsh and variable environments, including brackish and salt water (7–12), and to possess other beneficial traits for outdoor, large-scale, biofuel-relevant cultivation, as follows: it thrives in temperatures of 35 to 45°C (13–15), resists toxins (12) and grazers (16), accumulates microcrystalline guanine and polyphosphate (17) and lutein as an important coproduct for aquaculture (15), settles rapidly (13), and has diverse, sporopollenin-containing cell walls (18–20). Desmodesmus achieved areal harvest yield productivities of 9 to 20 g/m2 day (annual average of 11.4 g/m2 day) over the course of 2 years in outdoor, large-scale saltwater cultivation (2, 11, 21, 22) and can accumulate >55% dry cell weight (dcw) lipids (14, 23) or carbohydrates (13), both important cellular components for biofuels, making it amenable to a fractionation-based conversion pathway (24–26). Here, we report the draft nuclear and chloroplast genomes, ploidy, and potential bioenergy-relevant engineering targets of D. armatus.

D. armatus (Fig. 1), originally isolated from Las Cruces, NM, wastewater treatment ponds in 2012, was grown photoautotrophically in flat-sided bottles in modified artificial seawater medium (MASM) under constant illumination (4000K LED flat panels, 180 μmol photons/m2), supplemented with 2% CO2. MASM contains the following (g/liter): NaCl (8), MgSO4·7H2O (2.5), KCl (0.6), NaNO3 (0.85), CaCl2·2H2O (0.3), Tris (1), KH2PO4 (0.05), NH4Cl (0.03), thiamine-HCl (3.5 mM stock; 1 ml/liter), cyanocobalamin (10 μg/L stock; 1 ml), and trace element stock (6 ml/liter). Trace element stock was made up of the following (g/liter): Na2-EDTA (1.0), FeCl3·6H2O (0.2), MnCl2·4H2O (0.072), ZnCl2 (0.02), Na2MoO4·2H2O (0.013), and CoCl2·6H2O (0.004). Genomic DNA was extracted from midexponential cells as described (27). PacBio sequence data consisted of average polymerase reads of 741,936 ± 76,024 bp, having a mean insert length of 6,026 ± 784 bp and generating a total assembly size of 116.31 Mb in 906 contigs with an N50 value of 341,806 bp and a GC content of 56.6%, and was determined to be diploid (28). This compares with the genomes of Tetradesmus obliquus (108.72 Mb; 29) and Scenedesmus obliquus (207.97 Mb; 30). Sixteen scaffolds (totaling 112,885 bp) contain chloroplast sequences identified using BLASTN against published chloroplast genomes for Chlorella vulgaris C-27 (31) and Monoraphidium neglectum (32). Proteins that may be beneficial for a robust, outdoor, bioenergy-relevant alga were identified. The presence of homologs of Chlamydomonas reinhardtii STT7 and LHCSR1/3 and the dioxygen reductases Flv3 and PTOX confirms the ability for state transition and nonphotochemical quenching processes involved in energy dissipation essential for maintaining photosynthetic electron transport chain integrity in high or fluctuating irradiances (33) and may be useful targets for the improvement of photosynthetic efficiency and harvest yields in open ponds. Polyphosphate kinase was also identified, suggesting polyphosphate production as an energy or phosphate reserve. In conclusion, the innate robustness and proven reliability of D. armatus in outdoor mass culture provides a robust yet flexible chassis for genetic engineering efforts, potentially leading to the commercial use of D. armatus as a bioenergy-relevant alga.

FIG 1.

FIG 1

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Typical cenobium with terminal spines and intracellular changes in morphology of D. armatus under nitrogen-replete and -deplete (inset) conditions. Nitrogen-deplete conditions occur in late-stage cultures once nitrogen is depleted from the medium.

Data availability.

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number VIIQ00000000.

ACKNOWLEDGMENTS

We are grateful for the contribution of this strain and associated data from Craig Behnke at Sapphire Energy. This work was authored in part by the National Renewable Energy Laboratory, operated by the Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under contract number DE-AC36-08GO28308. We acknowledge Nick Sweeney of NREL for the micrographs of D. armatus.

Funding was provided by the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy and by the Rewiring Algal Carbon Energetics for Renewables (RACER) consortium. Additional support was provided by the National Renewable Energy Laboratory Research Data Initiative.

The views expressed in the article do not necessarily represent the views of the DOE or the U.S. Government.

This research was designed by E.P.K. and L.M.L.M., E.P.K., and D.P.A. directed the PacBio sequencing and assembly. A.N. determined ploidy. D.D. identified proteins of interest.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number VIIQ00000000.

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