Differential interference contrast light micrograph showing girdle and valve views of Nitzschia inconspicua GAI-293 cells of various sizes in growth phase. Photo credit: Aga Pinowska, Global Algae Innovations.

Fluorescence micrograph of cells stained with Nile Red (red – chlorophyll autofluorescence, yellow – stained non polar lipid droplets). Photo credit: Aga Pinowska, Global Algae Innovations.

The genome and transcriptome sequences were not determined by the Joint Genome Institute (JGI). The genome was sequenced with PacBio, assembled with Canu, and annotated with Braker2 by Aaron Oliver at the University of California San Diego. The transcriptome was sequenced with Illumina by Tyson Burch at the Colorado School of Mines, and then assembled with Trinity by Oliver. In order to ensure this genome is comparable to those sequenced by the JGI, the JGI Annotation Pipeline applied filters to remove: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, 4) alleles on secondary scaffolds and 5) unsupported short models. These removals generated the FilteredModels1 gene track. All of Oliver's original Braker2 models are available in the ExternalModels track. The JGI Annotation Pipeline was used to add functional annotation to this genome.

Diatoms are common algae in aquatic benthic systems. They are important primary producers and form the base of many benthic aquatic food webs in marine, freshwater and brackish aquatic environments.

Genus Nitzschia is distributed all over the globe. Nitzschia is potentially an important species for aquaculture, especially for benthic feeding organisms such as shrimp. Nitzschia produces ω-3 fatty acids including eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA).

Nitzschia inconspicua GAI-293 is a benthic and tychoplanktonic species isolated from a tidal stream in Hawaii. It can grow in a wide range of salinities. It is of special interest for algae biofuels production due to its high growth rate, good lipid production, resistance to contamination by other species of algae and also to many predators. It can form auxospores through self fertilization – a critical characteristic for a commercial diatom strain where cell size reduction can be a large problem for strains without self fertilization capability.

To our knowledge this is the first complete genome of a benthic diatom that can grow in a wide range of salinities.