Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production

Roth, Melissa S.; Cokus, Shawn J.; Gallaher, Sean D.; Walter, Andreas; Lopez, David; Erickson, Erika; Endelman, Benjamin; Westcott, Daniel; Larabell, Carolyn A.; Merchant, Sabeeha S.; Pellegrini, Matteo; Niyogi, Krishna K.

doi:10.1073/pnas.1619928114

Title: Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production

Journal Article · Mon May 08 00:00:00 EDT 2017 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1619928114· OSTI ID:1355950

Roth, Melissa S.; Cokus, Shawn J.; Gallaher, Sean D.; Walter, Andreas; Lopez, David; Erickson, Erika; Endelman, Benjamin; Westcott, Daniel; Larabell, Carolyn A.; Merchant, Sabeeha S.; Pellegrini, Matteo;

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231; GBMF3070; FC02-02ER63421; 2013-67012-21272

OSTI ID:: 1355950

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Vol. 114 Journal Issue: 21; ISSN 0027-8424

Publisher:: National Academy of Sciences, Washington, DC (United States)Copyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 106 works

Citation information provided by
Web of Science

References (48)

The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex Blanc, Guillaume; Duncan, Garry; Agarkova, Irina The Plant Cell, Vol. 22, Issue 9 https://doi.org/10.1105/tpc.110.076406	journal	September 2010
Three Acyltransferases and Nitrogen-responsive Regulator Are Implicated in Nitrogen Starvation-induced Triacylglycerol Accumulation in Chlamydomonas Boyle, Nanette R.; Page, Mark Dudley; Liu, Bensheng Journal of Biological Chemistry, Vol. 287, Issue 19 https://doi.org/10.1074/jbc.M111.334052	journal	March 2012
Photosystem II Subunit PsbS Is Involved in the Induction of LHCSR Protein-dependent Energy Dissipation in Chlamydomonas reinhardtii Correa-Galvis, Viviana; Redekop, Petra; Guan, Katharine Journal of Biological Chemistry, Vol. 291, Issue 33 https://doi.org/10.1074/jbc.M116.737312	journal	June 2016
A Dynein Light Chain Is Essential for the Retrograde Particle Movement of Intraflagellar Transport (IFT) Pazour, Gregory J.; Wilkerson, Curtis G.; Witman, George B. The Journal of Cell Biology, Vol. 141, Issue 4 https://doi.org/10.1083/jcb.141.4.979	journal	May 1998
Stress-related differential expression of multiple β-carotene ketolase genes in the unicellular green alga Haematococcus pluvialis Huang, Jun-Chao; Chen, Feng; Sandmann, Gerhard Journal of Biotechnology, Vol. 122, Issue 2 https://doi.org/10.1016/j.jbiotec.2005.09.002	journal	March 2006
Astaxanthin, a Carotenoid with Potential in Human Health and Nutrition Hussein, Ghazi; Sankawa, Ushio; Goto, Hirozo Journal of Natural Products, Vol. 69, Issue 3 https://doi.org/10.1021/np050354+	journal	December 2005
Accumulation of astaxanthin and lutein in Chlorella zofingiensis (Chlorophyta) Del Campo, J. A.; Rodr�guez, H.; Moreno, J. Applied Microbiology and Biotechnology, Vol. 64, Issue 6 https://doi.org/10.1007/s00253-003-1510-5	journal	June 2004
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes Cantarel, B. L.; Korf, I.; Robb, S. M. C. Genome Research, Vol. 18, Issue 1 https://doi.org/10.1101/gr.6743907	journal	November 2007
Transcriptome analysis of Chlorella zofingiensis to identify genes and their expressions involved in astaxanthin and triacylglycerol biosynthesis Huang, Weiping; Ye, Jingrun; Zhang, Jingjing Algal Research, Vol. 17 https://doi.org/10.1016/j.algal.2016.05.015	journal	July 2016
Total Internal Reflection Fluorescence (TIRF) Microscopy of Chlamydomonas Flagella Engel, Benjamin D.; Lechtreck, Karl-Ferdinand; Sakai, Tsuyoshi Methods in Cell Biology https://doi.org/10.1016/S0091-679X(08)93009-0	book	January 2009
Genome-Based Examination of Chlorophyll and Carotenoid Biosynthesis in Chlamydomonas reinhardtii Lohr, Martin; Im, Chung-Soon; Grossman, Arthur R. Plant Physiology, Vol. 138, Issue 1 https://doi.org/10.1104/pp.104.056069	journal	April 2005
Synthetic astaxanthin is significantly inferior to algal-based astaxanthin as an antioxidant and may not be suitable as a human nutraceutical supplement Capelli, Bob; Bagchi, Debasis; Cysewski, Gerald R. Nutrafoods, Vol. 12, Issue 4 https://doi.org/10.1007/s13749-013-0051-5	journal	December 2013
An ancient light-harvesting protein is critical for the regulation of algal photosynthesis Peers, Graham; Truong, Thuy B.; Ostendorf, Elisabeth Nature, Vol. 462, Issue 7272 https://doi.org/10.1038/nature08587	journal	November 2009
Carotenoids in Algae: Distributions, Biosyntheses and Functions Takaichi, Shinichi Marine Drugs, Vol. 9, Issue 6 https://doi.org/10.3390/md9061101	journal	June 2011
Potential health-promoting effects of astaxanthin: A high-value carotenoid mostly from microalgae Yuan, Jian-Ping; Peng, Juan; Yin, Kai Molecular Nutrition & Food Research, Vol. 55, Issue 1 https://doi.org/10.1002/mnfr.201000414	journal	November 2010
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Simão, Felipe A.; Waterhouse, Robert M.; Ioannidis, Panagiotis Bioinformatics, Vol. 31, Issue 19 https://doi.org/10.1093/bioinformatics/btv351	journal	June 2015
Repbase Update, a database of repetitive elements in eukaryotic genomes Bao, Weidong; Kojima, Kenji K.; Kohany, Oleksiy Mobile DNA, Vol. 6, Issue 1 https://doi.org/10.1186/s13100-015-0041-9	journal	June 2015
Accumulation of Secondary Carotenoids in Chlorella zofingiensis Rise, Moshe; Cohen, Ephraim; Vishkautsan, Marina Journal of Plant Physiology, Vol. 144, Issue 3 https://doi.org/10.1016/S0176-1617(11)81189-2	journal	September 1994
Utilization of cane molasses towards cost-saving astaxanthin production by a Chlorella zofingiensis mutant Liu, Jin; Sun, Zheng; Zhong, Yujuang Journal of Applied Phycology, Vol. 25, Issue 5 https://doi.org/10.1007/s10811-013-9974-x	journal	January 2013
Mutational and Functional Analysis of the -Carotene Ketolase Involved in the Production of Canthaxanthin and Astaxanthin Ye, R. W.; Stead, K. J.; Yao, H. Applied and Environmental Microbiology, Vol. 72, Issue 9 https://doi.org/10.1128/AEM.00918-06	journal	September 2006
Secondary ketocarotenoid astaxanthin biosynthesis in algae: a multifunctional response to stress Lemoine, Yves; Schoefs, Benoît Photosynthesis Research, Vol. 106, Issue 1-2 https://doi.org/10.1007/s11120-010-9583-3	journal	August 2010
Enhancement of carotenoids biosynthesis in Chlamydomonas reinhardtii by nuclear transformation using a phytoene synthase gene isolated from Chlorella zofingiensis Cordero, Baldo F.; Couso, Inmaculada; León, Rosa Applied Microbiology and Biotechnology, Vol. 91, Issue 2 https://doi.org/10.1007/s00253-011-3262-y	journal	April 2011
Light stress and photoprotection in Chlamydomonas reinhardtii Erickson, Erika; Wakao, Setsuko; Niyogi, Krishna K. The Plant Journal, Vol. 82, Issue 3 https://doi.org/10.1111/tpj.12825	journal	March 2015
An Outlook on Microalgal Biofuels Wijffels, R. H.; Barbosa, M. J. Science, Vol. 329, Issue 5993, p. 796-799 https://doi.org/10.1126/science.1189003	journal	August 2010
The Occurrence of the psbS Gene Product in Chlamydomonas reinhardtii and in Other Photosynthetic Organisms and Its Correlation with Energy Quenching ^† Bonente, Giulia; Passarini, Francesca; Cazzaniga, Stefano Photochemistry and Photobiology, Vol. 84, Issue 6 https://doi.org/10.1111/j.1751-1097.2008.00456.x	journal	November 2008
Genetic engineering of the green alga Chlorella zofingiensis: a modified norflurazon-resistant phytoene desaturase gene as a dominant selectable marker Liu, Jin; Sun, Zheng; Gerken, Henri Applied Microbiology and Biotechnology, Vol. 98, Issue 11 https://doi.org/10.1007/s00253-014-5593-y	journal	March 2014
Phylogeny and Molecular Evolution of the Green Algae Leliaert, Frederik; Smith, David R.; Moreau, Hervé Critical Reviews in Plant Sciences, Vol. 31, Issue 1 https://doi.org/10.1080/07352689.2011.615705	journal	January 2012
Intersection of Chlorella, Muriella and Bracteacoccus: Resurrecting the genus Chromochloris Kol et Chodat (Chlorophyceae, Chlorophyta). Fucikova, Karolina; Lewis, Louise A. Fottea, Vol. 12, Issue 1 https://doi.org/10.5507/fot.2012.007	journal	March 2012
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions Merchant, S. S.; Prochnik, S. E.; Vallon, O. Science, Vol. 318, Issue 5848, p. 245-250 https://doi.org/10.1126/science.1143609	journal	October 2007
The impact of nitrogen starvation on the dynamics of triacylglycerol accumulation in nine microalgae strains Breuer, Guido; Lamers, Packo P.; Martens, Dirk E. Bioresource Technology, Vol. 124 https://doi.org/10.1016/j.biortech.2012.08.003	journal	November 2012
Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution Fučíková, Karolina; Lewis, Paul O.; Lewis, Louise A. Molecular Phylogenetics and Evolution, Vol. 98 https://doi.org/10.1016/j.ympev.2016.01.022	journal	May 2016
Simultaneous production of triacylglycerol and high-value carotenoids by the astaxanthin-producing oleaginous green microalga Chlorella zofingiensis Liu, Jin; Mao, Xuemei; Zhou, Wenguang Bioresource Technology, Vol. 214 https://doi.org/10.1016/j.biortech.2016.04.112	journal	August 2016
PF15p Is the Chlamydomonas Homologue of the Katanin p80 Subunit and Is Required for Assembly of Flagellar Central Microtubules Dymek, Erin E.; Lefebvre, Paul A.; Smith, Elizabeth F. Eukaryotic Cell, Vol. 3, Issue 4 https://doi.org/10.1128/EC.3.4.870-879.2004	journal	August 2004
The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation Blanc, Guillaume; Agarkova, Irina; Grimwood, Jane Genome Biology, Vol. 13, Issue 5 https://doi.org/10.1186/gb-2012-13-5-r39	journal	January 2012
PredAlgo: A New Subcellular Localization Prediction Tool Dedicated to Green Algae Tardif, Marianne; Atteia, Ariane; Specht, Michael Molecular Biology and Evolution, Vol. 29, Issue 12 https://doi.org/10.1093/molbev/mss178	journal	July 2012
β-carotene is the intermediate exported from the chloroplast during accumulation of secondary carotenoids in Haematococcus pluvialis Grünewald, Kay; Hagen, Christoph Journal of Applied Phycology, Vol. 13, Issue 1, p. 89-93 https://doi.org/10.1023/A:1008183328839	journal	January 2001
Gene Arrangement Convergence, Diverse Intron Content, and Genetic Code Modifications in Mitochondrial Genomes of Sphaeropleales (Chlorophyta) Fučíková, Karolina; Lewis, Paul O.; González-Halphen, Diego Genome Biology and Evolution, Vol. 6, Issue 8 https://doi.org/10.1093/gbe/evu172	journal	August 2014
ISOLATION AND CHARACTERIZATION OF THE PHYTOENE DESATURASE GENE AS A POTENTIAL SELECTIVE MARKER FOR GENETIC ENGINEERING OF THE ASTAXANTHIN-PRODUCING GREEN ALGA CHLORELLA ZOFINGIENSIS (CHLOROPHYTA) Huang, Junchao; Liu, Jin; Li, Yantao Journal of Phycology, Vol. 44, Issue 3 https://doi.org/10.1111/j.1529-8817.2008.00511.x	journal	June 2008
Effect of biomass concentration on secondary carotenoids and triacylglycerol (TAG) accumulation in nitrogen-depleted Chlorella zofingiensis Mulders, Kim J. M.; Janssen, Jorijn H.; Martens, Dirk E. Algal Research, Vol. 6 https://doi.org/10.1016/j.algal.2014.08.006	journal	October 2014
Recent breakthroughs in the biology of astaxanthin accumulation by microalgal cell Solovchenko, Alexei E. Photosynthesis Research, Vol. 125, Issue 3 https://doi.org/10.1007/s11120-015-0156-3	journal	May 2015
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature, Vol. 408, Issue 6814, p. 796-815 https://doi.org/10.1038/35048692	journal	December 2000
HIGH-LIGHT AND SODIUM CHLORIDE STRESS DIFFERENTIALLY REGULATE THE BIOSYNTHESIS OF ASTAXANTHIN IN CHLORELLA ZOFINGIENSIS (CHLOROPHYCEAE) Li, Yantao; Huang, Junchao; Sandmann, Gerhard Journal of Phycology, Vol. 45, Issue 3 https://doi.org/10.1111/j.1529-8817.2009.00689.x	journal	June 2009
Enhanced production of astaxanthin by the green microalga Chlorella zofingiensis in mixotrophic culture Ip, Po-Fung; Wong, Ka-Ho; Chen, Feng Process Biochemistry, Vol. 39, Issue 11 https://doi.org/10.1016/j.procbio.2003.08.003	journal	July 2004
Cloning and selection of carotenoid ketolase genes for the engineering of high-yield astaxanthin in plants Huang, Junchao; Zhong, Yujuan; Sandmann, Gerhard Planta, Vol. 236, Issue 2 https://doi.org/10.1007/s00425-012-1654-6	journal	April 2012
Future prospects of microalgal biofuel production systems Stephens, Evan; Ross, Ian L.; Mussgnug, Jan H. Trends in Plant Science, Vol. 15, Issue 10 https://doi.org/10.1016/j.tplants.2010.06.003	journal	October 2010
Genetic Structure of the Mating-Type Locus of Chlamydomonas reinhardtii Ferris, Patrick J.; Armbrust, E. Virginia; Goodenough, Ursula W. Genetics, Vol. 160, Issue 1 https://doi.org/10.1093/genetics/160.1.181	journal	January 2002
Chlorella zofingiensis as an Alternative Microalgal Producer of Astaxanthin: Biology and Industrial Potential Liu, Jin; Sun, Zheng; Gerken, Henri Marine Drugs, Vol. 12, Issue 6 https://doi.org/10.3390/md12063487	journal	June 2014
Scale-up potential of cultivating Chlorella zofingiensis in piggery wastewater for biodiesel production Zhu, Liandong; Wang, Zhongming; Takala, Josu Bioresource Technology, Vol. 137 https://doi.org/10.1016/j.biortech.2013.03.144	journal	June 2013

Similar Records

Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production

Journal Article · Mon May 08 00:00:00 EDT 2017 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1355950

Roth, Melissa S.; Cokus, Shawn J.; Gallaher, Sean D.; +9 more

Regulation of Oxygenic Photosynthesis during Trophic Transitions in the Green Alga Chromochloris zofingiensis

Journal Article · Wed Feb 20 00:00:00 EST 2019 · The Plant Cell · OSTI ID:1355950

Roth, Melissa S.; Gallaher, Sean D.; Westcott, Daniel J.; +15 more

Systems Analysis and Engineering of Biofuel Production in Chromochloris zofingiensis, an Emerging Model Green Alga

Technical Report · Mon Mar 25 00:00:00 EDT 2024 · OSTI ID:1355950

Niyogi, Krishna K.; Blaby-Haas, Crysten; Boyle, Nanette; +4 more

Title: Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production

Citation Formats

References (48)

Similar Records

Related Subjects