Nannochloropsis oceanica strain:C018 Genome sequencing

Microalgae-based technologies have emerged as sustainable alternatives to mitigate the impact of rising CO2 emissions while providing industrial solutions applicable in agriculture, medicine, cosmetics, energy among others. Nannochloropsis algae exhibit high productivity, tolerance for elevated CO2 concentrations, thrive in outdoor conditions, have potential for biofuel production and have emerged as model organisms for applied phycology. Additionally, the biochemical characteristics of Nannochloropsis make them a valuable candidate as a food source for both animals and humans. Nannochloropsis oceanica C018 was provided by University of Hawaii-Manoa and taxonomically identified with 18S rRNA gene sequencing and analysis.Nannochloropsis oceanica C018 cultures were performed in 20L carboys with autoclaved filtered coastal seawater using F/2 medium on a 24 hour light cycle while bubbled with filtered air. DNA was isolated with DNA miniprep kit. High fidelity sequencing reads were obtained with Pacific Biosciences Revio system with version smrtlink 13 and ICS version 13 Libraries were prepared using Express Template Prep kit version 3 for standard HiFi library preparation. DNA fragments between 15-20 kb were selected for sequencing. 1,906,268 total reads were generated with an N50 value of 5090 bp, Hifi read yield was 11,001,781,445 bp, resulting in 415x coverage for the 26.5 Mbp genome.Genome assembly was performed following a modified version of the VGP pipeline in usegalaxy.org. Samtools v.1.15.1 was used to extract fastq files from bam files, Cutadapt v.4.6. was implemented to trim adapter sequences and filter low quality reads. Hifiasm v.0.19.8 was used to assemble contigs from High fidelity reads. Resulting assembly was decontaminated with kraken2 v.2.1.1 and duplicates were purged with purge_dups v.1.2.6. Completeness of resulting genome was estimated with BUSCO v.5.5.0 and quality assessed with QUAST v.5.2.0.. Default parameters were used except where otherwise noted.The resulting genome assembly consisted of 34 contigs , a size of 26.51 Mbp (415x coverage) with a GC content of 54.26%, N50 value of 1.18 Mbp and a Busco completeness score of 94%.