Complete Genome Sequence of the Model Oleaginous Alga Nannochloropsis gaditana CCMP1894.

The model oleaginous alga Nannochloropsis gaditana was completely sequenced using a combination of optical mapping and next-generation sequencing technologies to generate one of the most complete eukaryotic genomes published to date. The assembled genome is 30.7 Mb long.

GENOME ANNOUNCEMENT

As the world moves away from fossil fuels to more sustainable and renewable energy sources, photosynthetic algae have shown great promise as a potential alternative liquid fuel. Nannochloropsis gaditana and other members of the genus Nannochloropsis have been extensively studied because of their natural ability to make lipids (1–3), and there have been several publications of draft whole-genome sequences, transcriptomes, and organelle genomes for this species (4–10). Recently, we published a doubling of lipid productivity in this species by decreasing the expression levels of a single transcription factor (11).

Nannochloropsis gaditana CCMP1894 was obtained from CCMP, now known as the National Center for Marine Algae and Microbiota (https://ncma.bigelow.org/), cell sorted to a single cell, and propagated to produce a clonal population. The strain was cultivated as described previously (9), and DNA was isolated by grinding with liquid nitrogen, followed by a general phenol-chloroform clean-up procedure. The genome was sequenced using PacBio single-molecule real-time (SMRT) sequencing technology. In addition, optical mapping (12) was used to generate chromosome size scaffolds and to aid in gap filling. Several PacBio SMRTbell libraries were made and sequenced on a total of 26 SMRT cells on the PacBio RS II platform, for a total of 8.86 Gb. The PacBio data were assembled using Hierarchical Genome Assembly Process 2 (HGAP2) into 92 nuclear contigs (after removal of 20 contigs, including the plastidial and mitochondrial contigs, as well as contigs determined to originate from bacterial contamination), and the resulting contig sequences were polished with Quiver. The polished assembled contigs were then mapped and assigned to chromosomes using an optical map obtained from OpGen (Gaithersburg, MD) as a reference. Out of the 92 nuclear contigs, 39 contigs were uniquely assigned to chromosomal positions. Further manual finishing resulted in the closure of 5 of the 9 remaining gaps.

The final assembly was 30.7 Mb long, and it consisted of 30 chromosomal scaffolds (29.98 Mb; 97.6%) and 53 unplaced contigs (725 kb; 2.4%). Out of the 30 chromosomal scaffolds, 23 scaffolds included both telomeric sequences and no gaps, 4 scaffolds included both telomeric sequences and a single gap each, and 3 scaffolds included one of the two telomeric sequences with no additional gaps. The earlier draft genome sequences of Nannochloropsis species have been useful for understanding the basic metabolic machinery and genes involved in important processes, such as lipid metabolism. However, these genomes were highly fragmented and are not suitable for understanding chromosome architecture or to effectively engineer chromosomes, and they almost certainly do not annotate a number of functional genes (11). This near-complete assembly will enable future studies to better understand lipid metabolism, carbon partitioning, and photosynthetic efficiency and the ability to manipulate chromosomes within this model oleaginous alga (13).

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number PEIC00000000.