Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

Unkefer, Clifford J.; Sayre, Richard T.; Magnuson, Jon K.; Anderson, Daniel B.; Baxter, Ivan; Blaby, Ian K.; Brown, Judith K.; Carleton, Michael; Cattolico, Rose Ann; Dale, Taraka; Devarenne, Timothy P.; Downes, C. Meghan; Dutcher, Susan K.; Fox, David T.; Goodenough, Ursula; Jaworski, Jan; Holladay, Jonathan E.; Kramer, David M.; Koppisch, Andrew T.; Lipton, Mary S.; Marrone, Babetta L.; McCormick, Margaret; Molnár, István; Mott, John B.; Ogden, Kimberly L.; Panisko, Ellen A.; Pellegrini, Matteo; Polle, Juergen; Richardson, James W.; Sabarsky, Martin; Starkenburg, Shawn R.; Stormo, Gary D.; Teshima, Munehiro; Twary, Scott N.; Unkefer, Pat J.; Yuan, Joshua S.; Olivares, José A.

doi:10.1016/j.algal.2016.06.002

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

Journal Article · Wed Mar 01 04:00:00 EST 2017 · Algal Research

DOI:https://doi.org/10.1016/j.algal.2016.06.002· OSTI ID:1356499

Unkefer, Clifford J.; Sayre, Richard T.; Magnuson, Jon K.; Anderson, Daniel B.; Baxter, Ivan; Blaby, Ian K.; Brown, Judith K.; Carleton, Michael; Cattolico, Rose Ann; Dale, Taraka; Devarenne, Timothy P.; Downes, C. Meghan; Dutcher, Susan K.; Fox, David T.; Goodenough, Ursula; Jaworski, Jan; Holladay, Jonathan E.; Kramer, David M.; Koppisch, Andrew T.; Lipton, Mary S. more »

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortiumbegan, littlewas known about themolecular basis of algal biomass or oil production. Very fewalgal genome sequenceswere available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played bymetabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1356499

Report Number(s):: PNNL-SA-125672; 40890; BM0102030

Journal Information:: Algal Research, Journal Name: Algal Research Vol. 22; ISSN 2211-9264

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

References (83)

Forty Years of Bacterial Fatty Acid Synthesis Rock, Charles O.; Jackowski, Suzanne Biochemical and Biophysical Research Communications, Vol. 292, Issue 5 https://doi.org/10.1006/bbrc.2001.2022	journal	April 2002
Botryococcus braunii: a rich source for hydrocarbons and related ether lipids Metzger, P.; Largeau, C. Applied Microbiology and Biotechnology, Vol. 66, Issue 5 https://doi.org/10.1007/s00253-004-1779-z	journal	December 2004
A Comprehensive GC–MS Sub‐Microscale Assay for Fatty Acids and its Applications Bigelow, Nicholas W.; Hardin, William R.; Barker, James P. Journal of the American Oil Chemists' Society, Vol. 88, Issue 9 https://doi.org/10.1007/s11746-011-1799-7	journal	March 2011
Optimization of photosynthetic light energy utilization by microalgae Perrine, Zoee; Negi, Sangeeta; Sayre, Richard T. Algal Research, Vol. 1, Issue 2, p. 134-142 https://doi.org/10.1016/j.algal.2012.07.002	journal	October 2012
Chrysochromulina sp.: A proposed lipid standard for the algal biofuel industry and its application to diverse taxa for screening lipid content Bigelow, Nicholas; Barker, James; Ryken, Scott Algal Research, Vol. 2, Issue 4 https://doi.org/10.1016/j.algal.2013.07.001	journal	October 2013
Isoprenoid biosynthesis in eukaryotic phototrophs: A spotlight on algae Lohr, Martin; Schwender, Jörg; Polle, Jürgen E. W. Plant Science, Vol. 185-186 https://doi.org/10.1016/j.plantsci.2011.07.018	journal	April 2012
Biodiesel from microalgae beats bioethanol Chisti, Yusuf Trends in Biotechnology, Vol. 26, Issue 3 https://doi.org/10.1016/j.tibtech.2007.12.002	journal	March 2008
Hydrocarbon content and its relationship to physiological state in the green alga Botryococcus braunii Brown, A. C.; Knights, B. A.; Conway, Elsie Phytochemistry, Vol. 8, Issue 3 https://doi.org/10.1016/s0031-9422(00)85397-2	journal	March 1969
Proteomic Profiles of Five Strains of Oxygenic Photosynthetic Cyanobacteria of the Genus Cyanothece Aryal, Uma K.; Callister, Stephen J.; McMahon, Benjamin H. Journal of Proteome Research, Vol. 13, Issue 7 https://doi.org/10.1021/pr5000889	journal	June 2014
National microalgae biofuel production potential and resource demand: NATIONAL ALGAE BIOFUEL PRODUCTION Wigmosta, Mark S.; Coleman, André M.; Skaggs, Richard J. Water Resources Research, Vol. 47, Issue 3 https://doi.org/10.1029/2010wr009966	journal	March 2011
Genome sequencing in microfabricated high-density picolitre reactors Margulies, Marcel; Egholm, Michael; Altman, William E. Nature, Vol. 437, Issue 7057, p. 376-380 https://doi.org/10.1038/nature03959	journal	July 2005
Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropsis gaditana Radakovits, Randor; Jinkerson, Robert E.; Fuerstenberg, Susan I. Nature Communications, Vol. 3, Issue 1 https://doi.org/10.1038/ncomms1688	journal	January 2012
Nutritional Control of Sexuality in Chlamydomonas Reinhardi Sager, Ruth; Granick, S. Journal of General Physiology, Vol. 37, Issue 6 https://doi.org/10.1085/jgp.37.6.729	journal	July 1954
Identifying bacterial genes and endosymbiont DNA with Glimmer Delcher, Arthur L.; Bratke, Kirsten A.; Powers, Edwin C. Bioinformatics, Vol. 23, Issue 6 https://doi.org/10.1093/bioinformatics/btm009	journal	January 2007
High-throughput functional annotation and data mining with the Blast2GO suite Gotz, S.; Garcia-Gomez, J. M.; Terol, J. Nucleic Acids Research, Vol. 36, Issue 10 https://doi.org/10.1093/nar/gkn176	journal	April 2008
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
Phosphate Regulation of Lipid Biosynthesis in Arabidopsis Is Independent of the Mitochondrial Outer Membrane DGS1 Complex Moellering, Eric R.; Benning, Christoph Plant Physiology, Vol. 152, Issue 4 https://doi.org/10.1104/pp.110.153262	journal	February 2010
A Lipid Droplet Protein of Nannochloropsis with Functions Partially Analogous to Plant Oleosins Vieler, Astrid; Brubaker, Shane B.; Vick, Bertrand Plant Physiology, Vol. 158, Issue 4 https://doi.org/10.1104/pp.111.193029	journal	February 2012
Systems-Level Analysis of Nitrogen Starvation-Induced Modifications of Carbon Metabolism in a Chlamydomonas reinhardtii Starchless Mutant Blaby, I. K.; Glaesener, A. G.; Mettler, T. The Plant Cell, Vol. 25, Issue 11 https://doi.org/10.1105/tpc.113.117580	journal	November 2013
The Path to Triacylglyceride Obesity in the sta6 Strain of Chlamydomonas reinhardtii Goodenough, Ursula; Blaby, Ian; Casero, David Eukaryotic Cell, Vol. 13, Issue 5 https://doi.org/10.1128/ec.00013-14	journal	February 2014
Genomic Screening with RNAi: Results and Challenges Mohr, Stephanie; Bakal, Chris; Perrimon, Norbert Annual Review of Biochemistry, Vol. 79, Issue 1 https://doi.org/10.1146/annurev-biochem-060408-092949	journal	June 2010
A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes Starkenburg, Shawn R.; Kwon, Kyungyoon J.; Jha, Ramesh K. BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-212	journal	January 2014
Synthetic Routes to Methylerythritol Phosphate Pathway Intermediates and Downstream Isoprenoids Jarchow-Choy, Sarah; Koppisch, Andrew; Fox, David Current Organic Chemistry, Vol. 18, Issue 8 https://doi.org/10.2174/1385272819666140501001101	journal	June 2014
Expression of Genes in Cyanobacteria: Adaptation of Endogenous Plasmids as Platforms for High-Level Gene Expression in Synechococcus sp. PCC 7002 Xu, Yu; Alvey, Richard M.; Byrne, Patrick O. Methods in Molecular Biology, p. 273-293 https://doi.org/10.1007/978-1-60761-925-3_21	book	September 2010
The flanking regions of PsaD drive efficient gene expression in the nucleus of the green alga Chlamydomonas reinhardtii Fischer, N.; Rochaix, J. -D. Molecular Genetics and Genomics, Vol. 265, Issue 5 https://doi.org/10.1007/s004380100485	journal	April 2001
Evaluation of ionic liquids on phototrophic microbes and their use in biofuel extraction and isolation Lovejoy, Katherine S.; Davis, Lauren E.; McClellan, Lisa M. Journal of Applied Phycology, Vol. 25, Issue 4 https://doi.org/10.1007/s10811-012-9907-0	journal	September 2012
Theoretical Maximum Algal Oil Production Weyer, Kristina M.; Bush, Daniel R.; Darzins, Al BioEnergy Research, Vol. 3, Issue 2 https://doi.org/10.1007/s12155-009-9046-x	journal	October 2009
Escherichia coli as a model for the regulation of dissociable (type II) fatty acid biosynthesis Rock, Charles O.; Cronan, John E. Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism, Vol. 1302, Issue 1 https://doi.org/10.1016/0005-2760(96)00056-2	journal	July 1996
Fluorometric determination of the neutral lipid content of microalgal cells using Nile Red Cooksey, Keith E.; Guckert, James B.; Williams, Scott A. Journal of Microbiological Methods, Vol. 6, Issue 6 https://doi.org/10.1016/0167-7012(87)90019-4	journal	September 1987
Hydrocarbon content and its relationship to physiological state in the green alga Botryococcus braunii Brown, A. C.; Knights, B. A.; Conway, Elsie Phytochemistry, Vol. 8, Issue 3 https://doi.org/10.1016/S0031-9422(00)85397-2	journal	March 1969
MicroRNAs Bartel, David P. Cell, Vol. 116, Issue 2 https://doi.org/10.1016/S0092-8674(04)00045-5	journal	January 2004
Initial risk assessment of genetically modified (GM) microalgae for commodity-scale biofuel cultivation Henley, William J.; Litaker, R. Wayne; Novoveská, Lucie Algal Research, Vol. 2, Issue 1 https://doi.org/10.1016/j.algal.2012.11.001	journal	January 2013
Responsible Approaches to Genetically Modified Microalgae Production Olivares, José A.; Wijffels, René H. Algal Research, Vol. 2, Issue 1 https://doi.org/10.1016/j.algal.2013.01.002	journal	January 2013
Glycogen synthesis is a required component of the nitrogen stress response in Synechococcus elongatus PCC 7942 Hickman, Jason W.; Kotovic, Kimberly M.; Miller, Cameron Algal Research, Vol. 2, Issue 2 https://doi.org/10.1016/j.algal.2013.01.008	journal	March 2013
Evaluating nuclear transgene expression systems in Chlamydomonas reinhardtii Kumar, Anil; Falcao, Vanessa R.; Sayre, Richard T. Algal Research, Vol. 2, Issue 4 https://doi.org/10.1016/j.algal.2013.09.002	journal	October 2013
The environmental photobioreactor (ePBR): An algal culturing platform for simulating dynamic natural environments Lucker, Ben F.; Hall, Christopher C.; Zegarac, Robert Algal Research, Vol. 6 https://doi.org/10.1016/j.algal.2013.12.007	journal	October 2014
Metabolic and cellular organization in evolutionarily diverse microalgae as related to biofuels production Hildebrand, Mark; Abbriano, Raffaela M.; Polle, Juergen EW Current Opinion in Chemical Biology, Vol. 17, Issue 3 https://doi.org/10.1016/j.cbpa.2013.02.027	journal	June 2013
Molecular characterization of a bifunctional glyoxylate cycle enzyme, malate synthase/isocitrate lyase, in Euglena gracilis Nakazawa, Masami; Minami, Tomomi; Teramura, Koji Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, Vol. 141, Issue 4 https://doi.org/10.1016/j.cbpc.2005.05.006	journal	August 2005
TAG, You’re it! Chlamydomonas as a reference organism for understanding algal triacylglycerol accumulation Merchant, Sabeeha S.; Kropat, Janette; Liu, Bensheng Current Opinion in Biotechnology, Vol. 23, Issue 3 https://doi.org/10.1016/j.copbio.2011.12.001	journal	June 2012
The single cellular green microalga Botryococcus braunii, race B possesses three distinct 1-deoxy-d-xylulose 5-phosphate synthases Matsushima, Daisuke; Jenke-Kodama, Holger; Sato, Yohei Plant Science, Vol. 185-186 https://doi.org/10.1016/j.plantsci.2012.01.002	journal	April 2012
Supermatrix Data Highlight the Phylogenetic Relationships of Photosynthetic Stramenopiles Yang, Eun Chan; Boo, Ga Hun; Kim, Hee Jeong Protist, Vol. 163, Issue 2 https://doi.org/10.1016/j.protis.2011.08.001	journal	March 2012
Microalgae for biodiesel production and other applications: A review Mata, Teresa M.; Martins, António A.; Caetano, Nidia. S. Renewable and Sustainable Energy Reviews, Vol. 14, Issue 1, p. 217-232 https://doi.org/10.1016/j.rser.2009.07.020	journal	January 2010
Highway or byway: the metabolic role of the GABA shunt in plants Fait, Aaron; Fromm, Hillel; Walter, Dirk Trends in Plant Science, Vol. 13, Issue 1 https://doi.org/10.1016/j.tplants.2007.10.005	journal	January 2008
Chlamydomonas starchless mutant defective in ADP-glucose pyrophosphorylase hyper-accumulates triacylglycerol Li, Yantao; Han, Danxiang; Hu, Guongrong Metabolic Engineering, Vol. 12, Issue 4, p. 387-391 https://doi.org/10.1016/j.ymben.2010.02.002	journal	July 2010
Methods and applications for assembling large DNA constructs Merryman, Chuck; Gibson, Daniel G. Metabolic Engineering, Vol. 14, Issue 3 https://doi.org/10.1016/j.ymben.2012.02.005	journal	May 2012
Foot-and-mouth disease virus VP1 protein fused with cholera toxin B subunit expressed in Chlamydomonas reinhardtii chloroplast Sun, Meng; Qian, Kaixian; Su, Ning Biotechnology Letters, Vol. 25, Issue 13, p. 1087-1092 https://doi.org/10.1023/A:1024140114505	journal	July 2003
National microalgae biofuel production potential and resource demand: NATIONAL ALGAE BIOFUEL PRODUCTION Wigmosta, Mark S.; Coleman, André M.; Skaggs, Richard J. Water Resources Research, Vol. 47, Issue 3 https://doi.org/10.1029/2010WR009966	journal	March 2011
Full-length transcriptome assembly from RNA-Seq data without a reference genome Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran Nature Biotechnology, Vol. 29, Issue 7 https://doi.org/10.1038/nbt.1883	journal	May 2011
Hybrid error correction and de novo assembly of single-molecule sequencing reads Koren, Sergey; Schatz, Michael C.; Walenz, Brian P. Nature Biotechnology, Vol. 30, Issue 7 https://doi.org/10.1038/nbt.2280	journal	July 2012
Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs Bartel, David P.; Chen, Chang-Zheng Nature Reviews Genetics, Vol. 5, Issue 5 https://doi.org/10.1038/nrg1328	journal	May 2004
Transformation of the diatom Phaeodactylum tricornutum (Bacillariophyceae) with a variety of selectable marker and reporter genes Zaslavskaia, Lioudmila A.; Lippmeier, J. Casey; Kroth, Peter G. Journal of Phycology, Vol. 36, Issue 2 https://doi.org/10.1046/j.1529-8817.2000.99164.x	journal	April 2000
The Metabolome of Chlamydomonas reinhardtii following Induction of Anaerobic H ₂ Production by Sulfur Depletion Matthew, Timmins; Zhou, Wenxu; Rupprecht, Jens Journal of Biological Chemistry, Vol. 284, Issue 35 https://doi.org/10.1074/jbc.M109.003541	journal	May 2009
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
S -Adenosyl-L-homocysteine Hydrolase, Key Enzyme of Methylation Metabolism, Regulates Phosphatidylcholine Synthesis and Triacylglycerol Homeostasis in Yeast : IMPLICATIONS FOR HOMOCYSTEINE AS A RISK FACTOR OF ATHEROSCLEROSIS Malanovic, Nermina; Streith, Ingo; Wolinski, Heimo Journal of Biological Chemistry, Vol. 283, Issue 35, p. 23989-23999 https://doi.org/10.1074/jbc.M800830200	journal	June 2008
Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics Xie, Fang; Liu, Tao; Qian, Wei-Jun Journal of Biological Chemistry, Vol. 286, Issue 29 https://doi.org/10.1074/jbc.R110.199703	journal	June 2011
Botryococcus braunii : A Renewable Source of Hydrocarbons and Other Chemicals Banerjee, Anirban; Sharma, Rohit; Chisti, Yusuf Critical Reviews in Biotechnology, Vol. 22, Issue 3 https://doi.org/10.1080/07388550290789513	journal	January 2002
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Robinson, M. D.; McCarthy, D. J.; Smyth, G. K. Bioinformatics, Vol. 26, Issue 1 https://doi.org/10.1093/bioinformatics/btp616	journal	November 2009
Functional characterization of the three genes encoding 1-deoxy-D-xylulose 5-phosphate synthase in maize Cordoba, E.; Porta, H.; Arroyo, A. Journal of Experimental Botany, Vol. 62, Issue 6 https://doi.org/10.1093/jxb/erq393	journal	January 2011
The Pfam protein families database Finn, R. D.; Tate, J.; Mistry, J. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm960	journal	December 2007
APD2: the updated antimicrobial peptide database and its application in peptide design Wang, Guangshun; Li, Xia; Wang, Zhe Nucleic Acids Research, Vol. 37, Issue suppl_1 https://doi.org/10.1093/nar/gkn823	journal	October 2008
Acetyl-CoA Carboxylase in Higher Plants: Most Plants Other Than Gramineae Have Both the Prokaryotic and the Eukaryotic Forms of This Enzyme Konishi, T.; Shinohara, K.; Yamada, K. Plant and Cell Physiology, Vol. 37, Issue 2 https://doi.org/10.1093/oxfordjournals.pcp.a028920	journal	March 1996
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
A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii: A revised mineral nutrient supplement for Chlamydomonas Kropat, Janette; Hong-Hermesdorf, Anne; Casero, David The Plant Journal, Vol. 66, Issue 5 https://doi.org/10.1111/j.1365-313X.2011.04537.x	journal	March 2011
Presence of Glyoxylate Cycle Enzymes in the Mitochondria of Euglena gracilis Ono, Kouki; Kondo, Maki; Osafune, Tetsuaki The Journal of Eukaryotic Microbiology, Vol. 50, Issue 2 https://doi.org/10.1111/j.1550-7408.2003.tb00239.x	journal	March 2003
Real-Time DNA Sequencing from Single Polymerase Molecules Eid, John; Fehr, Adrian; Gray, Jeremy Science, Vol. 323, Issue 5910, p. 133-138 https://doi.org/10.1126/science.1162986	journal	January 2009
Comparing Photosynthetic and Photovoltaic Efficiencies and Recognizing the Potential for Improvement Blankenship, R. E.; Tiede, D. M.; Barber, J. Science, Vol. 332, Issue 6031, p. 805-809 https://doi.org/10.1126/science.1200165	journal	May 2011
Peptide Antimicrobial Agents Jenssen, Håvard; Hamill, Pamela; Hancock, Robert E. W. Clinical Microbiology Reviews, Vol. 19, Issue 3 https://doi.org/10.1128/CMR.00056-05	journal	July 2006
The Path to Triacylglyceride Obesity in the sta6 Strain of Chlamydomonas reinhardtii Goodenough, Ursula; Blaby, Ian; Casero, David Eukaryotic Cell, Vol. 13, Issue 5 https://doi.org/10.1128/EC.00013-14	journal	February 2014
Algal Lipid Bodies: Stress Induction, Purification, and Biochemical Characterization in Wild-Type and Starchless Chlamydomonas reinhardtii Wang, Zi Teng; Ullrich, Nico; Joo, Sunjoo Eukaryotic Cell, Vol. 8, Issue 12 https://doi.org/10.1128/EC.00272-09	journal	October 2009
Structural Correlates of Cytoplasmic and Chloroplast Lipid Body Synthesis in Chlamydomonas reinhardtii and Stimulation of Lipid Body Production with Acetate Boost Goodson, Carrie; Roth, Robyn; Wang, Zi Teng Eukaryotic Cell, Vol. 10, Issue 12 https://doi.org/10.1128/EC.05242-11	journal	October 2011
The roles of peptidyl-proline isomerases in gene regulation ¹ This review is part of Special Issue entitled Asilomar Chromatin and has undergone the Journal’s usual peer review process. Dilworth, David; Gudavicius, Geoff; Leung, Andrew Biochemistry and Cell Biology, Vol. 90, Issue 1 https://doi.org/10.1139/o11-045	journal	February 2012
MicroRNAs AND THEIR REGULATORY ROLES IN PLANTS Jones-Rhoades, Matthew W.; Bartel, David P.; Bartel, Bonnie Annual Review of Plant Biology, Vol. 57, Issue 1 https://doi.org/10.1146/annurev.arplant.57.032905.105218	journal	June 2006
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data Lopez, David; Casero, David; Cokus, Shawn J. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-282	journal	January 2011
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome Li, Bo; Dewey, Colin N. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-323	journal	August 2011
Bio-crude transcriptomics: Gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa)* Molnár, István; Lopez, David; Wisecaver, Jennifer H. BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-576	journal	January 2012
The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles Hovde, Blake T.; Starkenburg, Shawn R.; Hunsperger, Heather M. BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-604	journal	January 2014
Oil accumulation in the model green alga Chlamydomonas reinhardtii: characterization, variability between common laboratory strains and relationship with starch reserves Siaut, Magali; Cuiné, Stéphan; Cagnon, Caroline BMC Biotechnology, Vol. 11, Issue 1 https://doi.org/10.1186/1472-6750-11-7	journal	January 2011
Comparative energetics and kinetics of autotrophic lipid and starch metabolism in chlorophytic microalgae: implications for biomass and biofuel production Subramanian, Sowmya; Barry, Amanda N.; Pieris, Shayani Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-150	journal	January 2013
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides Berendzen, Joel; Bruno, William J.; Cohn, Judith D. BMC Research Notes, Vol. 5, Issue 1 https://doi.org/10.1186/1756-0500-5-460	journal	January 2012
Robust Expression and Secretion of Xylanase1 in Chlamydomonas reinhardtii by Fusion to a Selection Gene and Processing with the FMDV 2A Peptide Rasala, Beth A.; Lee, Philip A.; Shen, Zhouxin PLoS ONE, Vol. 7, Issue 8 https://doi.org/10.1371/journal.pone.0043349	journal	August 2012
Solexa Ltd Bennett, Simon Pharmacogenomics, Vol. 5, Issue 4 https://doi.org/10.1517/14622416.5.4.433	journal	June 2004
Microalgae: The Potential for Carbon Capture Sayre, Richard BioScience, Vol. 60, Issue 9 https://doi.org/10.1525/bio.2010.60.9.9	journal	October 2010
Chaperones and foldases in endoplasmic reticulum stress signaling in plants Gupta, Dinesh; Tuteja, Narendra Plant Signaling & Behavior, Vol. 6, Issue 2 https://doi.org/10.4161/psb.6.2.15490	journal	February 2011

Cited By (11)

Transcriptomic analysis of Chlorella sp. HS2 suggests the overflow of acetyl‐CoA and NADPH cofactor induces high lipid accumulation and halotolerance Yun, Jin‐Ho; Pierrelée, Michaël; Cho, Dae‐Hyun Food and Energy Security, Vol. 10, Issue 1 https://doi.org/10.1002/fes3.267	journal	December 2020
Using Flow Cytometry and Multistage Machine Learning to Discover Label-Free Signatures of Algal Lipid Accumulation Tanhaemami, Mohammad; Alizadeh, Elaheh; Sanders, Claire K. https://doi.org/10.1101/497834	posted_content	June 2019
Transcriptomic responses associated with carbon and energy flows under high salinity stress suggest the overflow of acetyl-CoA from glycolysis and NADPH co-factor induces high lipid accumulation and halotolerance in Chlorella sp. HS2 Yun, Jin-Ho; Pierrelée, Michaël; Cho, Dae-Hyun https://doi.org/10.1101/817551	posted_content	October 2019
Draft Nuclear Genome, Complete Chloroplast Genome, and Complete Mitochondrial Genome for the Biofuel/Bioproduct Feedstock Species Scenedesmus obliquus Strain DOE0152z Starkenburg, S. R.; Polle, J. E. W.; Hovde, B. Genome Announcements, Vol. 5, Issue 32 https://doi.org/10.1128/genomea.00617-17	journal	August 2017
Quantum Yield and Fatty Acid Profile Variations With Nutritional Mode During Microalgae Cultivation Rohit, M. V.; Venkata Mohan, S. Frontiers in Bioengineering and Biotechnology, Vol. 6 https://doi.org/10.3389/fbioe.2018.00111	journal	September 2018
Down-Selection and Outdoor Evaluation of Novel, Halotolerant Algal Strains for Winter Cultivation Dahlin, Lukas R.; Van Wychen, Stefanie; Gerken, Henri G. Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.01513	journal	October 2018
Advanced genetic tools enable synthetic biology in the oleaginous microalgae Nannochloropsis sp. Poliner, Eric; Farré, Eva M.; Benning, Christoph Plant Cell Reports, Vol. 37, Issue 10 https://doi.org/10.1007/s00299-018-2270-0	journal	March 2018
Algae-based sorbents for removal of gallium from semiconductor manufacturing wastewater Li, Mengling; Shadman, Farhang; Ogden, Kimberly L. Clean Technologies and Environmental Policy, Vol. 20, Issue 4 https://doi.org/10.1007/s10098-018-1497-3	journal	January 2018
Using flow cytometry and multistage machine learning to discover label-free signatures of algal lipid accumulation Tanhaemami, Mohammad; Alizadeh, Elaheh; Sanders, Claire K. Physical Biology, Vol. 16, Issue 5 https://doi.org/10.1088/1478-3975/ab2c60	journal	July 2019
Molecular Genetic Tools and Emerging Synthetic Biology Strategies to Increase Cellular Oil Content in Chlamydomonas reinhardtii Kong, Fantao; Yamaoka, Yasuyo; Ohama, Takeshi Plant and Cell Physiology, Vol. 60, Issue 6 https://doi.org/10.1093/pcp/pcz022	journal	January 2019
Nuclear, Chloroplast, and Mitochondrial Genome Sequences of the Prospective Microalgal Biofuel Strain Picochlorum soloecismus Gonzalez-Esquer, C. Raul; Twary, Scott N.; Hovde, Blake T. Genome Announcements, Vol. 6, Issue 4 https://doi.org/10.1128/genomea.01498-17	journal	January 2018

Similar Records

Related Subjects

Algal biology
Environmental Molecular Sciences Laboratory
Genomics
Lipid biosynthesis
NAABB
National Alliance for advanced biofuels and Bioproducts
Proteomics

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

Citation Formats

References (83)

Cited By (11)

Similar Records

Related Subjects