Status
[April 2024] Nannochloropsis oceanica C018 genome and transcriptome sequences were not determined by the Joint Genome Institute (JGI), but were provided by Adrian Graf and Zackary Johnson at Duke University. The genome was sequenced using PacBio Revio. High fidelity PacBio reads were assembled using Hifiasm v.0.19.8 with “light” purge level, and the transcriptome was assembled using Stringtie v.2.2.0. The assembly was then annotated using the JGI annotation pipeline.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 26.41 |
| Sequencing read coverage depth | |
| # of contigs | 30 |
| # of scaffolds | 30 |
| # of scaffolds >= 2Kbp | 30 |
| Scaffold N50 | 10 |
| Scaffold L50 (Mbp) | 1.18 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 1.67, 1.54, 1.47 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 58586781 | 58580341 | 100.0% |
| Other | RNA_contigs | 8684 | 8655 | 99.7% |
- Note: RNA reads were filtered based on mapping to the genome assembly.
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 3039 | 2208 |
| transcript | 2469 | 1723 |
| exon | 650 | 219 |
| intron | 205 | 167 |
| description: | ||
| protein length (aa) | 524 | 415 |
| exons per gene | 3.80 | 3 |
| # of gene models | 8768 |
Collaborators
- Adrian Estrada-Graf at Duke University, NC, USA
- Zackary Johnson at Duke University, NC, USA
Links
- JGI EcoGroup Portals: Algae Oceanic phytoplankton
- JGI PhyloGroup Portals: Heterokonta Ochrophyta Eustigmatophyta
Funding
The work conducted by the U.S. Department of Energy Joint Genome
Institute, a DOE Office of Science User Facility, is supported by
the Office of Science of the U.S. Department of Energy under
Contract No. DE-AC02-05CH11231.
