title: Genome and methylome of the oleaginous diatomCyclotella crypticareveal genetic flexibility toward a high lipid phenotype.
abstract: BACKGROUND
  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 diatomCyclotella 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.
  
  
  RESULTS
  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 inC. crypticathat 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.
  
  
  CONCLUSIONS
  Functional annotation and detailed cross-species comparison of key carbon rich processes inC. crypticahighlights 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.
authors.affiliation: Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA.
authors.forename: Jesse C
authors.initials: JC
authors.lastname: Traller
authors.affiliation: Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA.
authors.forename: Shawn J
authors.initials: SJ
authors.lastname: Cokus
authors.affiliation: Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Lopez
authors.affiliation: Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA.
authors.forename: Olga
authors.initials: O
authors.lastname: Gaidarenko
authors.affiliation: Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA ; J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA.
authors.forename: Sarah R
authors.initials: SR
authors.lastname: Smith
authors.affiliation: J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA.
authors.forename: John P
authors.initials: JP
authors.lastname: McCrow
authors.affiliation: Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA ; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA.
authors.forename: Sean D
authors.initials: SD
authors.lastname: Gallaher
authors.affiliation: Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA.
authors.forename: Sheila
authors.initials: S
authors.lastname: Podell
authors.affiliation: Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Thompson
authors.affiliation: Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA.
authors.forename: Orna
authors.initials: O
authors.lastname: Cook
authors.affiliation: Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA.
authors.forename: Marco
authors.initials: M
authors.lastname: Morselli
authors.affiliation: Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA.
authors.forename: Artur
authors.initials: A
authors.lastname: Jaroszewicz
authors.affiliation: Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA.
authors.forename: Eric E
authors.initials: EE
authors.lastname: Allen
authors.affiliation: Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA ; J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA.
authors.forename: Sabeeha S
authors.initials: SS
authors.lastname: Merchant
authors.affiliation: Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA.
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.affiliation: Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Hildebrand
keywords: Algae biofuel; Carbon metabolism; Cyclotella cryptica; DNA methylation; Diatom; Genome sequence