BER Structural Biology and Imaging Resources
Synchrotron, Neutron, and Cryo-EM
U.S. Department of Energy | Office of Science | Office of Biological and Environmental Research

Sequencing of Green Alga Genome Provides Blueprint to Advance Clean Energy, Bioproducts

April 12, 2017

Feature Story

Chromoshloris zofingiensis cell morphology. Cryo-soft X-ray tomography of a reconstructed cell with segmented nucleus (purple), chloroplast (green), mitochondria (red), lipids (yellow), and starch granules within the chloroplast (blue). (A) A representative orthoslice of the reconstructed cell. (B) Three-dimensional segmentation over two orthogonal orthoslices. (C) Segmented chloroplast and nucleus. (D) Fully segmented cell. [Reprinted with permission from Roth, M. S., et al. “Chromosome-Level Genome Assembly and Transcriptome of the Green Alga Chromochloris zofingiensis Illuminates Astaxanthin Production.” PNAS 114(21), E4296–E4305 (2017). [DOI:10.1073/pnas.1619928114]. Image credit Melissa S. Roth, HHMI/UC-Berkely and Andreas Walter, LBNL]

Microalgae have potential to help meet energy and food demands without exacerbating environmental problems. The unicellular green alga Chromochloris zofingiensis produces lipids for biofuels and a highly valuable carotenoid nutraceutical, astaxanthin. Thus advanced understanding of its biology is needed to facilitate commercial development. The assembly of the C. zofingiensis chromosome-level nuclear genome, organelle genomes, and transcriptome from diverse growth conditions was derived from a combination of short- and long-read sequencing in conjunction with optical mapping, revealing a compact genome of ~58 Mbp distributed over 19 chromosomes containing 15,274 predicted protein-coding genes. Found in the genome were 2 genes encoding beta-ketolase (BKT), the key enzyme synthesizing astaxanthin, and both were up-regulated by high light. Isolation and molecular analysis of astaxanthin-deficient mutants. Moreover, the transcriptome under high light exposure revealed candidate genes that could be involved in critical yet missing steps of astaxanthin biosynthesis, including ABC transporters, cytochrome P450 enzymes, and an acyltransferase. The high-quality genome and transcriptome provide insight into the green algal lineage and carotenoid production. Microalgae are a promising source of sustainable bioproducts for the increasing demand for food and energy without exacerbating worsening environmental problems. The algae have potential for use as a biofuel feedstock and nutraceutical molecules, including the carotenoid astaxanthin. Analyses of the C. zofingiensis genome and transcriptome and experiments characterizing astaxanthin production advance understanding of algae and carotenoids and enhance the commercial potential of C. zofingiensis.

Roth, M. S., et al.. “Chromosome-Level Genome Assembly and Transcriptome of the Green Alga Chromochloris zofingiensis Illuminates Astaxanthin Production.” PNAS 114(21), E4296–E4305 (2017). [DOI:10.1073/pnas.1619928114].

Instruments and Facilities Used: Soft X-ray tomography at National Center for X-ray Tomography (NCXT), operated jointly by Berkeley Lab (LBNL) and University of California, San Francisco, at LBNL’s Advanced Light Source. Other techniques: whole-genome optical mapping, high light RNA sequencing, transcriptome sequencing, and long read sequencing.

Funding Acknowledgements: Cryo-soft x-ray tomography support: Office of Basic Energy Sciences (OBES) Chemical Sciences, Geosciences, and Biosciences Division (CSGBD), U.S. Department of Energy (DOE) Office of Science, under field work proposal SISGRKN. Whole-genome optical mapping and high light RNA sequencing support: OBES, DOE Office of Science CSGBD under field work proposal 449B. Transcriptome sequencing and long-read sequencing support: Agriculture and Food Research Initiative (AFRI) Competitive Grant 2013-67012-21272 from U.S. Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA; to M.S.R.). National Center for X-ray Tomography (NCXT), Lawrence Berkeley National Laboratory (LBNL), supported by National Institutes of Health’s (NIH) National Institute of General Medical Sciences (NIGMS) Grant P41GM103445 and DOE Office of Biological and Environmental Research (OBER) Grant DE-AC02-05CH11231. S.J.C., S.D.G., S.S.M., and M.P. support: cooperative agreement with OBER, DOE Office of Science, under Award DE-FC02-02ER63421. D.L. support: NIH T32 Training Fellowship in Genome Analysis 5T32HG002536–13, Eugene V. Cota-Robles Fellowship, and Fred Eiserling and Judith Lengyel Doctoral Fellowship. D.W. support: National Science Foundation (NSF) Graduate Research Fellowship. K.K.N., Investigator of Howard Hughes Medical Institute (HHMI) support: Gordon and Betty Moore Foundation through Grant GBMF3070.