Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0670-3) contains supplementary material, which is available to authorized users.
Highlights
Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell
Genome sequence determination and assembly Three libraries with different average insert lengths were prepared from purified C. cryptica genomic DNA (Additional file 1: Additional methods)
The first four in silico organellar prediction programs are developed for higher plants and other eukaryotes, but we have found their collective use to be suitable for some basic understanding of metabolic compartmentation in diatoms, when overlaid with coordinate expression patterns of particular genes [27, 32]
Summary
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. Developing technologies have increased the promise of algal biofuel to meet energy needs [2, 3]. These new advances were preceded by the US Department of Energy funded Aquatic Species Program (ASP) which produced pioneering work in aquaculture and large-scale. Diatoms (Bacillariophyta), which are naturally highly productive, accounted for ~60% of the top-performing species in a recommended list of biofuel production organisms produced by the ASP [4]
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