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Title: Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype

Abstract

Here, improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids. As a result, we sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol. The genome is comprised of highly methylated repetitive sequence, which does not significantly change under silicon starved lipid induction, and data further suggests the primary role of DNA methylation is to suppress DNA transposition. Annotation of pivotal glycolytic, lipid metabolism, and carbohydrate degradation processes reveal an expanded enzyme repertoire in C. cryptica that would allow for an increased metabolic capacity toward triacylglycerol production. Identification of previously unidentified genes, including those involved in carbon transport and chitin metabolism, provide potential targets for genetic manipulation of carbon flux to further increase its lipid phenotype. New genetic tools were developed, bringing this organism on a par with other microalgae in terms of genetic manipulation and characterization approaches. Furthermore, functional annotation and detailedmore » cross-species comparison of key carbon rich processes in C. cryptica highlights the importance of enzymatic subcellular compartmentation for regulation of carbon flux, which is often overlooked in photosynthetic microeukaryotes. The availability of the genome sequence, as well as advanced genetic manipulation tools enable further development of this organism for deployment in large-scale production systems.« less

Authors:
 [1];  [2];  [2];  [1];  [3];  [4];  [2];  [1];  [2];  [1];  [2];  [2];  [1];  [3];  [2];  [2];  [1]
  1. Univ. of California San Diego, La Jolla, CA (United States)
  2. Univ. of California, Los Angeles, CA (United States)
  3. Univ. of California San Diego, La Jolla, CA (United States); J. Craig Venter Institute, La Jolla, CA (United States)
  4. J. Craig Venter Institute, La Jolla, CA (United States)
Publication Date:
Research Org.:
Univ. of California, San Diego, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); USDOE Office of Energy Efficiency and Renewable Energy (EERE)
OSTI Identifier:
1361559
Grant/Contract Number:  
SC0012556; EE0001222; FC02-02ER63421; SC0008593
Resource Type:
Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; diatom; genome sequence; Cyclotella cryptica; algae biofuel; carbon metabolism; DNA methylation

Citation Formats

Traller, Jesse C., Cokus, Shawn J., Lopez, David A., Gaidarenko, Olga, Smith, Sarah R., McCrow, John P., Gallaher, Sean D., Podell, Sheila, Thompson, Michael, Cook, Orna, Morselli, Marco, Jaroszewicz, Artur, Allen, Eric E., Allen, Andrew E., Merchant, Sabeeha S., Pellegrini, Matteo, and Hildebrand, Mark. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. United States: N. p., 2016. Web. doi:10.1186/s13068-016-0670-3.
Traller, Jesse C., Cokus, Shawn J., Lopez, David A., Gaidarenko, Olga, Smith, Sarah R., McCrow, John P., Gallaher, Sean D., Podell, Sheila, Thompson, Michael, Cook, Orna, Morselli, Marco, Jaroszewicz, Artur, Allen, Eric E., Allen, Andrew E., Merchant, Sabeeha S., Pellegrini, Matteo, & Hildebrand, Mark. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. United States. doi:10.1186/s13068-016-0670-3.
Traller, Jesse C., Cokus, Shawn J., Lopez, David A., Gaidarenko, Olga, Smith, Sarah R., McCrow, John P., Gallaher, Sean D., Podell, Sheila, Thompson, Michael, Cook, Orna, Morselli, Marco, Jaroszewicz, Artur, Allen, Eric E., Allen, Andrew E., Merchant, Sabeeha S., Pellegrini, Matteo, and Hildebrand, Mark. Fri . "Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype". United States. doi:10.1186/s13068-016-0670-3. https://www.osti.gov/servlets/purl/1361559.
@article{osti_1361559,
title = {Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype},
author = {Traller, Jesse C. and Cokus, Shawn J. and Lopez, David A. and Gaidarenko, Olga and Smith, Sarah R. and McCrow, John P. and Gallaher, Sean D. and Podell, Sheila and Thompson, Michael and Cook, Orna and Morselli, Marco and Jaroszewicz, Artur and Allen, Eric E. and Allen, Andrew E. and Merchant, Sabeeha S. and Pellegrini, Matteo and Hildebrand, Mark},
abstractNote = {Here, improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids. As a result, we sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol. The genome is comprised of highly methylated repetitive sequence, which does not significantly change under silicon starved lipid induction, and data further suggests the primary role of DNA methylation is to suppress DNA transposition. Annotation of pivotal glycolytic, lipid metabolism, and carbohydrate degradation processes reveal an expanded enzyme repertoire in C. cryptica that would allow for an increased metabolic capacity toward triacylglycerol production. Identification of previously unidentified genes, including those involved in carbon transport and chitin metabolism, provide potential targets for genetic manipulation of carbon flux to further increase its lipid phenotype. New genetic tools were developed, bringing this organism on a par with other microalgae in terms of genetic manipulation and characterization approaches. Furthermore, functional annotation and detailed cross-species comparison of key carbon rich processes in C. cryptica highlights the importance of enzymatic subcellular compartmentation for regulation of carbon flux, which is often overlooked in photosynthetic microeukaryotes. The availability of the genome sequence, as well as advanced genetic manipulation tools enable further development of this organism for deployment in large-scale production systems.},
doi = {10.1186/s13068-016-0670-3},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 9,
place = {United States},
year = {2016},
month = {11}
}

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