Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotypeReport as inadecuate

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Biotechnology for Biofuels

, 9:258

First Online: 25 November 2016Received: 08 July 2016Accepted: 15 November 2016


BackgroundImprovement 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.

ResultsWe 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.

ConclusionsFunctional 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.

KeywordsDiatom Genome sequence Cyclotella cryptica Algae biofuel Carbon metabolism DNA methylation AbbreviationsAAK14816-likeputative glycerol-3-phosphate acyltransferase

ACCacetyl-CoA carboxylase

AGPAT1-acyl-glycerol-3-phosphate acyltransferase

ASPAquatic Species Program

ASWartificial Seawater

BGS1,3 β-glucan synthase

DGATdiacylglycerol acyltransferase

DGTTdiacylglycerol acyltransferase type 2

EDEntner Doudoroff


ENRenoyl-ACP reductase

FBAfructose bisphosphate aldolase

FBPfructose 1,6 bisphosphatase


GAPDHglyceraldehyde 3-phosphate dehydrogenase

3PGglycerate 3-phosphate


GPIglucose-6-phosphate isomerase

GPATglycerol-3-phosphate acyltransferase

HD3-hydroxyacyl-ACP dehydratase

KAR3-ketoacyl-ACP reductase

KAS3-ketoacyl-ACP synthase

LCLAT1lysocardiolipin acyltransferase 1

LPLATlysophospholipid acyltransferase

MATmalonyl-CoA-ACP transacylase

MDHmalate dehydrogenase

MEmalic enzyme

MGATmonoacylglycerol acyltransferase

NRnitrate reductase


PAPphosphatidic acid phosphatase

PDRPpyruvate phosphate dikinase regulatory protein


PEPCphosphoenolpyruvate carboxylase

PEPCKphosphoenolpyruvate carboxykinase

PEPSphosphoenolpyruvate synthase


PGAMphosphoglycerate mutase

PGKphosphoglycerate kinase


PKpyruvate kinase

PPCperiplastid compartment

PPDKpyruvate phosphate dikinase

PPPpentose phosphate pathway

PYCpyruvate carboxylase

RBHreciprocal best BLAST hit

SARStramenopile, Alveolata, Rhizaria supergroup


TPItriose phosphate isomerase

UAPUDP-N-acetylglucosamine pyrophosphorylase

UGPUTP-glucose-1-phosphate uridylyltransferase

Electronic supplementary materialThe online version of this article doi:10.1186-s13068-016-0670-3 contains supplementary material, which is available to authorized users.

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Author: Jesse C. Traller - Shawn J. Cokus - David A. Lopez - Olga Gaidarenko - Sarah R. Smith - John P. McCrow - Sean D. Gall


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